A first-half goal from midfielder Gary McDonald proved more than enough at Boundary Park and the Latics held on comfortably and could afford to miss other chances to increase their lead.
McDonald's strike was his first since arriving on a Bosman free transfer from the Scottish Premier League, where he turned down a new contract at Kilmarnock.
His winner carried Oldham out of the bottom four but left Scunthorpe manager Brian Laws voicing concern about the form of his struggling side.
Laws had changed a winning team, dropping Daniel McBreen from the starting 11 which beat Gillingham last week and replacing him with Andy Keogh.
But Scunthorpe created little up front and their boss later admitted, in hindsight, he may have made the wrong decision.
Oldham were on top from the start and almost led on 10 minutes when Will Haining set up Andy Liddell for a volley which flew inches wide of the post.
Striker Paul Warne forced a save from Joe Murphy before Scunthorpe had a bright spell of possession which they could not turn into any chances.
Oldham missed a clear opening just before the half-hour mark when the busy Liddell sent over a cross from the right and fellow winger Paul Edwards was unable to keep his shot under control from close range.
But the breakthrough came on 34 minutes when Chris Porter got in front of his marker on the edge of the box and flicked the ball onto McDonald, who headed it inside the far post from eight yards.
Experienced defender Simon Charlton was off target for Oldham after arriving late at the far post and another chance went begging through Porter.
Scunthorpe sent on McBreen as a substitute and went with three men up front but Oldham kept them at bay until the 69th minute.
Home goalkeeper Les Pogliacomi had not made a save until then but he dived full-length to his left to deny Ian Baraclough from 12 yards.
Oldham stayed on top in the closing stages and almost doubled their lead through sub Craig Rocastle.