Stubblefield attended Purdue University, located in West Lafayette, Indiana, where he played under head coach Joe Tiller. He played alongside future NFL player Kyle Orton and consensus All-American kicker-punter Travis Dorsch. As a redshirt freshman he led the Boilermakers with 73 receptions. In the 2001 Sun Bowl against Washington State, he tied a Sun Bowl record of nine receptions, and set a record with 196 receiving yards. He also scored two touchdowns and recorded a bowl record with a 244 all-purpose yards. He helped lead the Boilermakers to a second straight Sun Bowl appearance in 2002. As a junior in 2003, Stubblefield led the Big Ten Conference with 86 receptions. He totaled 835 yards and three touchdowns. He was a Second Team All-Big Ten selection.