In 1895 he signed for Lincoln City who were then in the Second Division of the English Football League, playing alongside his elder brother Matt.
In the 1897–98 season Gillespie was City's leading scorer with 18 goals in 30 games, helping the team to third in the second division, nine points behind winners Burnley.
With Gillespie's brother Matt having joined Newton Heath, they met on opposite sides in the Manchester derby until City's promotion.
As a consequence, Sam Ormerod resigned as Manchester City manager and was succeeded by Tom Maley, who strengthened the team by purchasing Billy Lot Jones, Sandy Turnbull and Jimmy Bannister and they immediately earned promotion in the 1902–03 season by winning the Second Division championship.
In the 1903–04 season, Gillespie was City's top league goalscorer with 18 goals as the team finished in second place in the First Division, three points behind champions Sheffield Wednesday.
City played Bolton Wanderers in the 1904 FA Cup Final and won 1–0 to win their first major trophy; the only goal of the game was scored by Billy Meredith.
At the end of the season the Football Association conducted an investigation into the financial activities of Manchester City and discovered that the team had been paying their players extra.