Wrexham became only the second team to win at Scunthorpe this season as two second-half goals sent them into the third round draw of the FA Cup.
The hosts, a division above Wrexham, went closest to opening the scoring in the first half through Andy Keogh.
But Wrexham controlled after the break and took a deserved lead when Mark Jones drilled home from 30 yards.
Kevin Smith hooked in the second on 65 minutes before Keogh's header was ruled out for offside.
Scunthorpe: Murphy, Byrne, Crosby, Foster, Hinds (Williams 72), Taylor, Sparrow, Baraclough, Morris (Torpey 67), Sharp, Keogh. Subs Not Used: Lillis, Mulligan, Goodwin.
Wrexham: Ingham, Roche, Pejic, Steve Evans, Mike Williams, Mark Jones, Danny Williams, Ferguson, Johnson (Ugarte 90), Llewellyn, Smith (McEvilly 77).
Subs Not Used: Michael Jones, Valentine, Crowell.
Goals: Mark Jones 49, Smith 66.
Ref: K Friend (Leicestershire).