Two goals in four first half minutes secured the win as Freddie Ladapo opened the scoring on 41 minutes.
The striker converted from the edge of the box whilst four minutes later, Lee Erwin netted from inside the box to make it two.
Latics dominated the second half proceedings and ground out the result to earn the first home league win of the season.
Manager Stephen Robinson made two changes to his squad from Saturday’s loss against Bolton Wanderers as Cameron Dummigan and Ladapo were handed starts.
It was a quiet opening to the game which would explode into life towards the end of the half.
Scunthorpe United went the closest to scoring in the opening five minutes but Sam Mantom’s shot was deflected wide.
Carl Winchester had Latics’ first chance of the game as he got onto a cross into the box from Erwin but he could not connect properly with his chance.
Dummigan’s presence on the right hand side added a lot of pace and energy to the side but his dangerous cross on 17 minutes was just cleared.
Midway through the half, Ladapo had a sighter from the edge of the box which forced a smart stop from the goalkeeper.
Athletic started to take a grip of the game and just before the half hour mark, good football in midfield saw the ball played out to Jamie Reckord who forced the goalkeeper to palm away a cross.
Minutes later, Latics had a huge shout for a penalty turned down by referee Darren England. Flynn received the ball in the box and was caught as he went past his man but the referee waved away the play.
Five minutes later, however, Scunthorpe United felt they should have been awarded a penalty as Neal Bishop fell to ground in the box under a challenge but again the referee said no. He would later be booked for his protests.
Latics continued to dominate and deservedly took the lead on 42 minutes through Ladapo.
After good football from Latics, the ball fell to Ladapo on the edge of the box who created space for himself and rifled the ball past Joe Anyon to give Robinson’s men the lead.
As the fourth official announced one minute of additional time, Latics extended their lead through Erwin.
The striker was played through on goal, he took it inside past his man and from 12 yards curled it around Anyon to send Latics into the break two goals ahead.
Athletic started the second half well, keeping the ball well and frustrating their opponents.
The Iron were forced to shoot from range as Mantom tested the palms of Connor Ripley, whilst at the other end, Latics still proved to be a threat.
After good work on the right, the ball sat up perfectly for Flynn to strike on the volley but Anyon pulled off a good save to deny the midfielder.
Athletic were defending manfully and not allowing the visitors time on the ball.
Robinson made changes to freshen up his team with Marc Klok and Darius Osei coming into the action.
With only 10 minutes of the game remaining, Latics could and maybe should have made it three with Flynn going close.
Dummigan crossed the ball into the box to the unmarked midfielder but he shot over from close range.
It was Latics who controlled the game and looked the more likely to extend their lead in the final minutes of the game.
Athletic were backed by the excellent support from the fans as they really got behind the players throughout the 90 minutes.
Deep into additional time, Flynn’s piece of magic almost paid off as his individual run saw him get to the byline and Mirfin almost netted an own goal, but Latics came away with the deserved win.
Oldham Athletic: Ripley, Dummigan, Clarke, Burgess, Reckord, Winchester (Klok 70’), Fane, Green, Flynn, Erwin (Mckay 88’), Ladapo (Osei 78’).
Subs not used: Kettings, Wilson, Banks, Jahraldo-Martin.
Scunthorpe United: Anyon, Wiseman, Wallace, Mirfin, Dawson, Madden, Morris, Bishop (Ness 75’), Hopper (Holmes 64’), Mantom (van Veen 59’), Townsend.
Subs not used: Kelsey, Smallwood, Goode, Sutton.
Goals: Oldham Athletic (Ladapo 42’, Erwin 45+1’) 2-0 Scunthorpe United
Attendance: 2,911 (394 visiting supporters)