Drafted by the New York Giants in the third round (83rd overall) of the 1987 NFL Draft, Baker played for the Giants his entire career from 1987 to 1992. Stephen played in Super Bowl XXI and Super Bowl XXV.

Also known as Stephen Baker "The Touchdown Maker," he won a championship ring with New York in Super Bowl XXV, when they defeated the Buffalo Bills 20-19. Baker caught two passes for 31 yards, including a 14-yard touchdown pass from Jeff Hostetler late in the 2nd quarter.

Baker finished his six NFL seasons with 141 receptions for 2,587 yards and 21 touchdowns, along with 21 rushing yards.

In 1992, according to Football Outsiders, Baker had the worst catch rate of any wide receiver from 1991–2011, catching only 28.8% of the passes thrown to him.

In 2008, Baker was inducted into the Fresno County Athletic Hall of Fame.^]