The second season of the television series Stargate Atlantis commenced airing on the Sci Fi Channel in the United States on July 15, 2005, concluded on The Movie Network in Canada on January 30, 2006, and contained 20 episodes.

Season two regular cast members include Joe Flanigan, Torri Higginson, Rachel Luttrell, Jason Momoa, Paul McGillion, and David Hewlett as Dr. Rodney McKay.

The second season focuses on the Atlantis Expedition continuing to make the Wraith think that the city self-destructed, (The Siege Part III) while continuing to explore Pegasus and hunt for ZPMs (although they do have one now) this means at times lying to new allies about the city even sometimes claiming to be a small contingent that escaped the Siege; the season also marks the first time the Expedition is able to make contact with Earth although doing so uses much power so the contact is oftentimes via the Daedalus, an intergalactic Earth-Asgard vessel commanded by Col. Steven Caldwell who makes clear his desire to be Military Leader of Atlantis but eventually settles for a sort of advisory role as it becomes clear that Dr. Weir and the Lt.Col Sheppard are a duo not to be messed with.

Season two regular cast members include Joe Flanigan, Torri Higginson, Rainbow Sun Francks, Rachel Luttrell, Jason Momoa and David Hewlett.

[10] For "Grace Under Pressure", Joel Goldsmith was nominated for an Emmy in the category "Outstanding Music Composition for a Series (Original Dramatic Score)".

[12] ComingSoon reviewer Scott Chitwood said that it "should satisfy" viewers, but commented that it didn't have the same quality as Battlestar Galactica and gave the series 6 out of 10 and the DVD package 8 out of 10.

[13] June L. from Monsters and Critics (M&C) gave the season 4 out of 5 and said that it was a "pleasure to watch the stories", compared to other new science fiction shows which depends on blood and violence.