 Henderson joined Mick Moody and John McDonnell in joining Shamrock Rovers.In September 2009, Henderson was inducted into the St. Pats hall of fame.Henderson stayed with Shamrock Rovers for only season, making 31 appearances and keeping 14 clean sheets, before joining crosstown rivals Bohemians where he played in every league game and finished top of the league table in his first season, 1992–93 League of Ireland Premier Division.