After ending his player career, Stoican started as coach for Minerul Valea Copcii. He managed CSM Reșița in the 2010–11 season and in July 2011 he came to Dinamo where he became responsible for the second team. After only six months, he resigned from Dinamo II and took control of Chindia Târgoviște. He resigned from Chindia in September 2012, following a poor serie of results.
In October 2012, Stoican became head coach at CS Mioveni, with a primary objective to help the team promote to Liga I.