McCrary returned to professional football in 1999 with the San Diego Chargers and for the first time played all 16 games in a season. With 14 starts, McCrary made 37 receptions for 201 yards and a touchdown in 1999. That touchdown was McCrary's first career receiving touchdown, in which Jim Harbaugh completed an 18-yard pass to McCrary on December 26 against the Oakland Raiders. In the final game of the season on January 2, 2000, a 12–6 win over the defending champion Denver Broncos, McCrary made 3 receptions for a season-high 39 receiving yards. McCrary earned the team Special Teams Player of the Year honor for 15 special teams tackles. On December 5, McCrary returned one kickoff for 4 yards.