The characters from the Canadian-American military science fiction television series Stargate Atlantis were created by Brad Wright and Robert C. Cooper. The series follows the adventures of a human expedition to the lost city of Atlantis in the Pegasus Galaxy. The Stargate has brought humanity into contact with other cultures, including new and powerful enemies: the Wraith, the Genii, and later the Asurans and a lost tribe of Asgard, all while trying to uncover the secrets the Ancients left behind.

Stargate Atlantis has a small cast, amounting to ten main cast actors over its five-season run. Most characters are introduced in outgoing expeditions outside the city of Atlantis.

John Sheppard played by Joe Flanigan is a USAF Lieutenant Colonel (ranked major in season 1). He is an experienced and a talented US Air Force Officer in Afghanistan, though his reputation is somewhat tarnished when he disobeyed a direct order in an unsuccessful attempt to save the lives of several US servicemen. When called upon to transport Brigadier General Jack O'Neill into the research base that has been established at the nearby Ancient defense facility, Sheppard inadvertently discovers that he not only has the ATA gene (the genetic factor necessary to activate Ancient technology), but that he is naturally proficient at using it. After some doubts, he finally joins the expedition to Atlantis, although Colonel Marshall Sumner makes it clear he is not pleased about Sheppard's involvement in the mission. In Season 1, Sheppard serves as both a Major and later also becomes the military commander following Colonel Sumner's death. In Season 2, Sheppard is eventually promoted to Lieutenant Colonel and still remains as Atlantis's military commander with Sheppard serving as the team leader for the Atlantis Expedition's team, the First Atlantis Reconnaissance Team or AR-1.

Dr. Elizabeth Weir played by Torri Higginson is the civilian and also the original leader of the Atlantis Expedition which she does for the first three years. Prior to joining the SGC, Weir was engaged to be married to a man named Simon Wallace but their engagement ended when Wallace refused to join the SGC. Weir originally served as the head of the SGC after General George Hammond was reassigned in the Stargate SG-1 Season 7 finale episode, "Lost City Part 1" with Weir serving in the role as SGC Commander up until her departure in the Stargate SG-1 Season 8 episode, "New Order Part 2" with Weir being replaced by newly promoted Brigadier General Jack O'Neill. After leaving the SGC, Weir heads to Antarctica to lead the research envoy studying the Ancient defense facility that had been discovered in Antarctica, the Ancient city of Atlantis which SG-1 had uncovered during "Lost City Part 2". Weir eventually leads the Atlantis Expedition which is sent through the Stargate to explore the Lost City of Atlantis. Weir is a diplomat and a leader, often making decisions in the hope they will benefit her and her people although she has clashed with others on occasions. In the Atlantis Season 3 finale episode, "First Strike", Weir is left in a coma when a beam that the Expeditions's enemies, the Asurans had created targets the Control Room of Atlantis. Weir survives although she becomes part-Replicator due to the fact that the nanites that were left in her system during the Stargate Atlantis Season 3 episode, "Progeny" have been reactivated. Weir eventually sacrifices herself to give Sheppard and his team enough time to escape during the Stargate Atlantis Season 4 episode, "Lifeline" with her fate being unknown although she later returns as a Replicator in the Season 5 episode, "Ghost in the Machine". Her position as leader of the Atlantis Expedition is later taken over by Lieutenant Colonel Samantha Carter and following Carter's return to Earth by Richard Woolsey.

Samantha "Sam" Carter played by Amanda Tapping is an astrophysicist and USAF colonel. Samantha Carter is a member of the SGC's flagship team, SG-1, having served there for ten years, with Carter herself having been under the rank of captain, major and then lieutenant colonel and later, at an unknown point after the end of the Ori conflict in Stargate SG-1, Carter is promoted to a "full bird" colonel and is transferred to the Midway space station to oversee the final stages of completion. The IOA appoints Carter as the new commander of the Atlantis expedition early in Season 4 of Atlantis. At the end of the first episode of season five, Carter is recalled to Earth for a Tok'ra extraction ceremony concerning the final Ba'al clone, with Richard Woolsey eventually replacing her as the new commander of the Atlantis Expedition.

Richard Woolsey played by Robert Picardo is a former member of the NID and the United States representative to the IOA. Richard Woolsey is part of an IOA panel that recalled Dr. Weir to Earth to explain her failed alliance with the Wraith. He genuinely respects Weir and attempts to defend her actions, but must defer to his IOA colleagues. The IOA dispatch him to Atlantis to evaluate Weir's ability to command. While evaluating Weir's abilities, he made a rather poor impression on the expedition members. However, he ultimately sides with Weir by sending the IOA a report modified to favor Weir and keep her in command of Atlantis. Woolsey later joins the Atlantis expedition on a permanent basis at the start of Season Five after his predecessor, Colonel Carter is reassigned.

Rodney McKay or Meredith Rodney McKay played by David Hewlett is the Chief Science Officer of the Atlantis expedition and a member of the main Expedition team, the First Atlantis Reconnaissance Team or AR-1. Dr. McKay is one of the most arrogant and condescending personalities in the Stargate franchise. He once identified himself as a Mensa member and believes himself to be the smartest person in the city, as mentioned in a conversation between Dr. Weir and Carson in "Hide and Seek". What makes it worse for his fellow team members is that, while he does not possess the wisdom of many of the other characters, in terms of raw intelligence or at least the occasional fits of insight/brilliance, he is. Despite his irritating demeanor, many members of the Atlantis expedition are on friendly terms with him, and McKay is able to keep steady relationships and is close to the people he works with, having referred to them as a surrogate family in a message to his estranged sister Jeannie Miller (played by David Hewlett's real-life younger sister, actress Kate Hewlett).

Ronon Dex played by Jason Momoa is a Satedan warrior and a member of the Satedan military where he held the rank of Specialist. Approximately seven years before Ronon's first contact with the Atlantis Expedition, the Wraith attacked Sateda. Ronon remained behind with Melena to fight the Wraith, but the Wraith defeated Satedan forces and Melena was killed before Ronon's eyes in an explosion. Ronon was later captured by the Wraith who instead of feeding on him turned him into a Runner, implanting a tracking device in his upper back and setting him loose to be constantly hunted. Ronon later becomes a permanent member of Sheppard's team, AR-1, replacing Aidan Ford who defects from Atlantis after Ford develops an addiction to the Wraith enzyme.