The 24-year-old struck on 36 minutes, confidently striking past the goalkeeper, and although having to do a lot of defending, Latics ground out the result and came away with the three points.
Latics started the game quite sluggishly as Fleetwood looked to take control of the game in the early proceedings.
The Cod Army should have been ahead in the opening two minutes of the game but Antoni Sarcevic’s strike from five yards went harmlessly over the crossbar.
With five minutes on the clock, Joel Coleman was forced into action as he tipped Stephan Jordan’s header past the post.
The visitors were really taking the game to Latics and this time Jamille Matt strikes over the crossbar from 20 yards under little pressure.
Latics needed a way back into the game but they were dealt a blow on 12 minutes as striker Jake Cassidy was forced off with a foot injury.
Rhys Turner was introduced into the action and he made an instant impact, nodding the ball down to Mike Jones to shoot from 25 yards but he struck over the crossbar.
Athletic were enjoying a lot more possession with Lee Croft, Dominic Poleon and Philliskirk looking particular highlights.
On the half hour mark Connor Brown flashed a ball across the box but it was just ahead of the onrushing strikers.
Athletic did take the lead ten minutes before half time through forward Philliskirk.
The striker controlled a long ball forward, stepped in-between the two Fleetwood Town defenders and knocked the ball beyond Chris Maxwell to give Latics the advantage.
The goal came slightly against the run of play but Latics seemed a lot more settled after the opener.
Athletic were forced into some defending at the end of the first half as Jordan went close with a header but they went into the half time break in the lead.
Fleetwood started the second half brightly and should have been level on 50 minutes. Bobby Grant stole a march on his defender but hit his shot straight at Coleman.
Minutes later, Latics could have extended their advantage through Croft. The winger, who is yet to score a goal for Latics, met a Joseph Mills cross six yards out but managed to sky his effort.
The Cod Army were peppering Coleman’s goal as Danny Andrew struck straight at the number one on 60 minutes whilst Grant also shot from 25 yards which was saved.
With the game starting to liven up, Eggert Jonsson and Jimmy Ryan were both booked for the Cod Army as they started to up the tempo in the game.
With Latics seemingly happy to sit on their one goal advantage, they were allowing Fleetwood time on the ball but the visitors were struggling to penetrate the stubborn Oldham back line.
David Dunn was introduced, replacing fellow substitute Rhys Turner, and he added that extra bit of experience to grind out the result.
With the visitors throwing everything forward in a bid to get something out of the game, young defender Jonathan Burn was impressing at the heart of the defence.
Deep into additional time, with Latics struggling to clear the danger, the ball bounced nervously around the box but the ball finally fell into the hands of Coleman to seal Darren Kelly’s first competitive win as manager of Oldham Athletic.
Oldham Athletic: Coleman, Brown, Burn, J.Wilson, Mills, Kelly, Jones, Philliskirk, Croft, Poleon (Forte 65’), Cassidy (Turner 12’, Dunn 76’).
Subs not used: Cornell, Dieng, Green, Winchester.
Fleetwood Town: Maxwell, McLaughlin, Andrew, Jordan, Jonsson, Bell, Ryan, Matt (Proctor 62’), Grant (Pond 86’), McManus (Ball 62’), Sarcevic.
Subs not used: Della-Verde, Forbes, Sowerby, Arestidou.
Goals: Oldham Athletic (Philliskirk 36’) 1-0 Fleetwood Town
Attendance: 4,139 (237 visiting supporters)