Clone Commanders, alternatively known as clone trooper commanders, represented a military rank within the Grand Army of the Republic. This rank was held by clone trooper officers who oversaw regiments composed of 2,304 troopers. Within each corps, the group of sixteen clone commanders were under the command of their corresponding Jedi General.
Advanced Recon Commandos who functioned as commanders were called Clone ARC Commanders. It was also possible for clone trooper pilots to hold commander positions. During the Clone Wars, Clone Commanders operated under the authority of Jedi Generals and, like their clone comrades, engaged in combat against the Confederacy of Independent Systems. As the war neared its conclusion, Supreme Chancellor Sheev Palpatine issued an order to all clones to turn against and eliminate their Jedi officers.
This rank persisted within the Imperial Military during the initial years of the Galactic Empire as clone troopers transitioned into the first generation of stormtroopers.

The designation of Clone Commander, also known as a clone trooper commander, signified a military rank conferred upon clone trooper officers throughout the period of the Clone Wars and the early Imperial Era. This rank was utilized by the Grand Army of the Republic, alongside both the Republic Navy and the Republic Starfighter Corps. Within the structure of the Galactic Republic, the title of Clone Commander was potentially awarded to clone trooper officers who simultaneously served as special ops clone troopers, Biker Advanced Recon Commandos, Clone SCUBA troopers, Advanced Recon Force Scout Troopers, among others.
Furthermore, clone trooper pilots and navigation officers were eligible to hold the rank, thereby exercising command over spatial operations as opposed to ground-based units. The importance of Clone Commanders sometimes warranted the assignment of personal guard details, where two clone troopers of lesser rank would protect their commanding officer by marching behind them. This rank later saw application in the initial stages of the Imperial Military, which began primarily as a clone-based force. During the early phases of Project War-Mantle's implementation, the rank even remained in use for recruited Elite Squad Troopers. However, as the Imperial Era progressed, the authority of Clone Commanders was gradually superseded by that of recruited officers; for example, a recruited lieutenant could issue directives and assignments to a Clone Commander.
Clone Commanders within the Republic Military typically underwent ARC training, although some, such as Ponds, did not receive this regimen. Despite this, Clone Commanders lacking ARC training could still be trained by veteran instructors to specialize in areas like military reconnaissance. Clone trooper officers were chosen for a program that taught them how to act as intermediaries between Jedi Generals and their clone trooper subordinates, although some Clone Commanders might not be included or briefed on interacting with Jedi high command.

In the beginning, Clone Commanders within the Army of the Republic were provided with standard Phase I clone trooper armor, distinguished by four yellow circles on the left chestplate, along with a yellow stripe running down each arm, vertically up the center of the helmet, and laterally around the visor.
Subsequently, Clone Commanders, like other clone officers, personalized their armor with additional gear, including kamas, pauldrons, rangefinders, secondary communication antennas, visors, jetpacks, pistol holsters, macrobinoculars, bandoliers, rank insignia plaques, built-in lights, primary communications antenna, unit affiliation markings, and more. Jaig Eyes could also be incorporated into the commander's armor. Phase II clone trooper armor allowed for even greater customization. Clone Commanders serving in the Republic Navy were equipped with a blue cloth fabric uniform, black gloves, and a rank insignia plaque.

The rank of Clone Commander represented the pinnacle of achievement for clone troopers, surpassing that of a Clone Captain. Several variations of the rank existed, including Clone Marshal Commander and Clone ARC Commander, reflecting the diverse roles and positions held by Clone Commanders. A Clone Marshal Commander served as the commanding officer of a corps within the Grand Army of the Republic, exemplified by Cody of the 7th Sky Corps, Bacara of the 21st Nova Corps, Neyo of the 91st Mobile Reconnaissance Corps, and Bly of the 327th Star Corps. Other commanders leading corps included Gree of the 41st Elite Corps and 9th Assault Corps.
Clone ARC Commanders were Advanced Recon Commandos who functioned as Clone Commanders. Multiple ARC Commanders could be assigned to the same unit, such as ARC Commanders Blitz, Colt, Havoc, and Hammer from the Rancor Battalion. Clone officers could be promoted to Clone Commander and placed in charge of either half of a legion or an entire division. A typical Clone Commander usually commanded a full regiment consisting of sixteen companies. One such commander was Tacks, who served throughout the Clone Wars.

Clone Commanders also had the capacity to command smaller military formations like battalions, which comprised four companies. Examples include Wolffe of the 104th Battalion, Jet of his own special operations battalion, and Crane of the One-Eighty-Fourth. Clone Commanders could also be in charge of specialized companies, such as Clone SCUBA troopers. Clone Commander Monnk commanded a company of such troopers during the war. Commanders like Ponds, who lacked training to directly serve under Jedi Generals, could still be appointed as their second-in-command. Ponds also acted as the commanding officer of Lightning Squadron, a light ground cavalry squadron.
Clone Commanders also served within the Republic Navy and the Republic's Starfighter Corps. A clone trooper pilot named Davijaan, also known as "Odd Ball," attained the rank of Clone Commander. Clone Commanders could function as the commanding officer of a Venator-class Star Destroyer or serve as part of its crew. Furthermore, Clone Commanders had the ability to lead an entire flight group, encompassing multiple squadrons and flights.

The rank of Clone Commander persisted within the Imperial Military during the early years of Sidious's reign as Galactic Emperor, as the clones continued to provide military service as the first generation of stormtroopers. Soon after the Galactic Republic was reorganized into the Galactic Empire, certain Clone Commanders were selected to lead new, experimental units composed of volunteers and conscripts instead of clones. The premier unit of this kind, the first Elite Squad, consisted of four Elite Squad Troopers under the command of Clone Commander Crosshair. The clone commando Scorch operated as a Clone Commander within the Advanced Science Division.

Clone Commanders received training from Jango Fett, who served as the clone template for the Republic's clone forces. Their initial deployment occurred during the First Battle of Geonosis, which involved numerous Clone Commanders. Although the members of the Jedi Order did not hold official ranks in the Republic Military at that time, the clone troopers and their commanders served under the Jedi who functioned as de facto generals on Geonosis. During the battle, Commander CT-411 reported to Jedi Master Mace Windu, who assumed command of five special commando units. While Windu and other Jedi engaged on the field, leading clone troopers against an army of battle droids, Grand Master Yoda oversaw the battle from the forward command center, where a Clone Commander kept him informed about the Republic Army's progress. Yoda commended the commander after receiving the report that the Separatist Droid Army was retreating.
Following the fall of Geonosis, the Grand Army of the Republic assembled on the Republic capital of Coruscant. Supreme Chancellor Sheev Palpatine, along with members of the Galactic Senate, observed the newly established Republic Military as Clone Commanders and their troops boarded the Acclamator-class transgalactic military assault ships, preparing to deploy across the galaxy to combat the forces of the Confederacy of Independent Systems.

Clone Commanders were assigned to Jedi Generals after the Jedi adopted the role of leadership in the Grand Army of the Republic. Relationships based on trust and mutual respect evolved between the commanders and their generals as they fought together throughout the numerous campaigns of the Clone Wars. General Obi-Wan Kenobi and Commander Cody served alongside each other as commanding officers of the 7th Sky Corps, including the 212th Attack Battalion. Cody displayed particular loyalty to Kenobi, who regarded the Clone Commander as a highly capable officer.
Clone Commander Wolffe and Jedi General Plo Koon also maintained a collaborative relationship throughout the Clone Wars. Despite the clones' perception of themselves as expendable due to their artificial nature, Koon valued their lives and risked his own to protect them. This resulted in a close bond with Wolffe. Under their leadership, the Wolfpack became one of the most esteemed clone trooper squads in the Grand Army of the Republic.

Despite Admiral Wilhuff Tarkin's reservations regarding leadership within the Republic Military, Clone Commanders and Jedi Generals continued to lead the armies of the Galactic Republic as the Clone Wars entered its final year. The Republic's strategy was now focused on eliminating the remaining Separatist forces in the Outer Rim Territories. Clone Commander Bly and Jedi General Aayla Secura oversaw the campaign on Felucia, while Clone Commander Bacara and Jedi General Ki-Adi-Mundi led the Republic assault on Mygeeto. Other battlefronts included Saleucami, where Clone Commander Neyo served alongside Jedi General Stass Allie, and Bracca, a Mid Rim planet that the 13th Battalion invaded under the command of Jedi General Jaro Tapal and his Clone Commander.
Following the Battle of Yerbana, Jedi General Anakin Skywalker committed half of the 501st Legion to the Siege of Mandalore, forming the 332nd Division, while the remaining forces returned to the Core Worlds to defend the capital during the Battle of Coruscant. The 332nd was created in response to Skywalker's former Padawan, Ahsoka Tano, who supported Lady Bo-Katan Kryze's efforts to reclaim Mandalore from the rogue Sith Lord Maul and his Mandalorian super commandos. However, as Tano had declined to rejoin the Jedi Order, she had forfeited her rank as a Jedi Commander and therefore could not officially lead Republic soldiers. Consequently, Skywalker promoted his second-in-command, Rex, to the rank of Clone Commander, granting the former Clone Captain the authority to lead the new division.

Following the successful defense of Coruscant, Clone Commander Gree and the 41st Scout Battalion accompanied Jedi Generals Yoda and Luminara Unduli to Kashyyyk, with the intention of protecting the strategically important homeworld of the Wookiee species. After Yoda's departure, Cody and Kenobi deployed their battalion to Utapau, where General Grievous had retreated after Count Dooku's death. However, following the Jedi High Council's failed attempt to arrest Chancellor Palpatine—who was revealed to be the Sith Lord Darth Sidious—after Grievous's destruction during the Battle of Utapau, the chancellor ordered the Clone Commanders and their clone troopers to execute Order 66, instantly turning the Jedi's own army against them.
Excluding the genetically defective clones of Clone Force 99, the behavioral modification biochips implanted within their brains compelled the vast majority of standard clone troopers to comply with Order 66, including those Clone Commanders who worked most closely with the Jedi Generals. Across the galaxy, Jedi were murdered by the soldiers and commanders whom they had trusted, including Mundi, who was killed by Bacara, and Secura, who was fatally shot in the back by Bly and his troops.

Clone Commanders also received strict orders from Sidious to eliminate any clone trooper who defied his plan to systematically purge the Jedi Order. However, the surgical removal of Rex's biochip enabled him to defend Ahsoka Tano against his own soldiers, who were still bound by their programming. Subsequently, his subordinate Clone Lieutenant Jesse accused him of committing treason against the Republic and declared that Rex would be demoted from the rank of Commander and executed. In response, Rex remarked to Tano that he had never liked being a Commander anyway. After becoming a fugitive from the Empire, which officially declared him dead, Rex reverted to using his former rank of Captain.

In the days following the establishment of the Galactic Empire, the rank of Clone Commander was conferred upon Crosshair, the sole member of Clone Force 99 who remained loyal to the Galactic Empire. Seeking to evaluate the initial results of Project War-Mantle, Admiral Tarkin instructed Commander Crosshair to take a squad of enlisted soldiers to Onderon and eliminate Saw Gerrera's insurgents.
ES-01, one of the natural-born human soldiers in Crosshair's squad, questioned the clone's fitness to serve as a commander, especially given the Empire's ongoing efforts to decommission the clone trooper program. However, Crosshair asserted his authority by executing ES-01 for refusing to complete the mission, which involved killing the civilians who were associated with Gerrera's group. The squad's success reinforced Vice Admiral Rampart's conviction that the Imperial Army could eventually be molded into the most formidable fighting force ever seen in galactic history, provided that non-clone soldiers continued to learn from the experience of veteran clones like Commander Crosshair.
Several months into the Empire's reign, Clone Marshal Commander Cody led a unit of clone stormtroopers in suppressing a Separatist holdout on the planet Desix. Having returned to the Empire despite being abandoned on Kamino during the Imperial withdrawal and attack, Crosshair, who had been stranded on the planet for thirty-two planetary rotations, was assigned to the squad. Although he initially anticipated leading the squad, Crosshair was not yet cleared to resume command but was pleased to work under Cody once more. However, Cody deserted after the mission, having become disillusioned with the Imperial cause.
Around 18 BBY, Clone Commander Mayday was killed in action during a failed attempt to recover Imperial supplies that had been stolen by insurgents on the planet Barton IV. Mayday's death proved to be the final catalyst for Crosshair's own disaffection with the Empire. Clone commando Scorch served in the Advanced Science Division as a Clone Commander but met his end during the skirmish on Wayland.