Craigan, 33, has become a regular in Nigel Worthington's side after making his debut in February 2003.
It is the fourth successive time he has worn the armband with Aaron Hughes standing down as his team-mate reaches his milestone.
Northern Ireland boss Worthington said: "Stephen will get his 50th and I am delighted for him.
"I have left him and Aaron to sort out the captain's armband but I think I know where it is going. He fully deserves it as well.
"Aaron has been outstanding when it comes to something like this. It is the sign of a good leader.
"I have known Stephen for the last three years and what you get from him is a solid performance.
"He is always there. He is a terrific servant, a fantastic professional and great to have around the group."