The 23-year-old son of former Great Britain loose forward Terry Flanagan has signed a two-year with Saints from 2012.
“I coached Mark previously at Wests Tigers,” said St Helens coach Royce Simmons. “He is a very good young British player who has benefited from his time in the NRL.
“He has an excellent attitude both on and off the field. He is tough and versatile and can play in the middle or on the edge. He can also cover at hooker if need be.”
The Oldham-born Flanagan made his Wigan debut in 2009 and went on to make 11 senior appearances before moving down under.