He is expected to be sidelined for three months, meaning Lillis will reprise his double act with McIlroy - he was his assistant at Northern Ireland and Stockport County - until well into the New Year.
Lillis, who is still a regular at Glanford Park as a guest summariser for BBC Radio Humberside and whose son is a YT at United, was assistant to current Scunthorpe boss Brian Laws when they won promotion via the Division Three play-offs in 1999.
But he quit to try his hand as manager of Halifax Town, with Russ Wilcox stepping into his shoes as No.2 to Laws.