McKellen appeared on Broadway in 2001 in "Dance of Death," while Stewart most recently appeared on Broadway in 2010 in "A Life in the Theatre."
Both productions will be limited-edition repertoires directed by Sean Mathias.
In "Waiting for Godot," Stewart will play Vladimir and McKellen will play Estragon in the classic tale of two men biding their time joking and arguing while they wait in vain for the mysterious Godot. "No Man's Land" will find Stewart and McKellen playing writers Hirst and Spooner, respectively.
Also read: Patrick Stewart Gets Torched for the London Olympics (Video)
Rehearsals for the productions — which are being produced by Stuart Thompson and NOMANGO Productions — will begin in the summer, after McKellen and Stewart complete filming on the upcoming "X-Men: Days of Future Past."
The productions will boast designs by Tony nominee Stephen Brimson Lewis ("Indiscretions") and lighting from Tony winner Peter Kaczorowski ("The Producers").
More details — such as the theater, production dates, schedule and additional casting — will be announced later.
McKellen and Stewart have performed together on stage before, in the 1977 premiere of Tom Stoppard's "Every Good Boy Deserves Favour."