With the 2005–06 season due to start, he became part of Adrian Boothroyd's reshaped Watford side, joining for a fee of £450,000. Signed the day before the first game of the season, he made his début and scored in the 2–1 loss to Preston North End which opened the season. Henderson went on to be an integral part of Watford's successful season in the Championship, scoring 14 goals – nine of which were headers – in 27 games as they finished third, including a splendid half-volley in the local derby away at Luton Town. He also scored a penalty in Watford's 3–0 win against Leeds United in the Championship play-off final, as Watford were promoted to the Premier League. A passionate player, Henderson amassed six yellow cards and one red in the 2005–06 season.