Jackson caught his first NFL touchdown on September 17, 2006, in a victory over the Tennessee Titans. In the Chargers' Christmas Eve game against the Seattle Seahawks, Jackson had a memorable touchdown catch that led the Chargers to victory. With 29 seconds left, quarterback Philip Rivers threw a touchdown pass to Jackson and the Chargers ended up winning the game 20–17 and setting a franchise record for wins. Jackson ended the season strongly and finished second on the team with six touchdown catches.