On 25 May 2015, O'Neill signed a two-year contract with Sydney FC.
O'Neill scored his first A-League goal in the Sydney Derby on Saturday 8 October 2016 by bending a free kick around the wall from just outside the penalty area into the top right corner. He scored his second goal of the season, also from a free kick against Melbourne City on Friday 24 February 2017 by curling the ball over the wall and into the top corner.
Following performances which made him a key member of the starting squad, Sydney FC re-signed O'Neill for another two years on 13 December 2016.
On 26 March 2017, O'Neill scored his third goal for Sydney FC away at Perth Glory, with a low and hard shot from outside the box, as the Sky Blues ran out 3–0 winners and secured the premiers plate.