As a defender, McDonnell started his career with Shamrock Rovers in the 1983–84 season (five total appearances), followed by Home Farm, Drogheda United before signing for Pats.
He then signed back for another spell at Richmond Park where he captained the side to the League triumph in the 1995–96 season under manager Brian Kerr.
His side initially struggled and only a late burst at the end of the 2005 season saw St. Pats saved from a humiliating relegation.
For the 2006 season, he assembled practically a whole new squad and reached the final of the FAI Cup losing to Derry City 4–3.
He then guided Pats to their best ever European run in the UEFA Cup in the 2008/2009 season where they qualified for the first round proper after eliminating JFK Olimps Riga and IF Elfsborg.
In September 2009, he returned to Irish League side Newry City as manager following the resignation of Gerry Flynn.