On 15 January 2009, O'Brien made the controversial move across Louth to Drogheda United's local rivals Dundalk who had just been promoted to the League of Ireland Premier Division.
He scored on his debut in the Europa League against Valletta[2] and repeated the trick in the second leg[3] to send St Patrick's Athletic into the next round.
O'Brien then scored in both rounds again against FC Krylia Sovetov Samara to become St Patrick's Athletic all-time record scorer in European competition at the time.
In December 2009, O'Brien joined Maltese football club Valletta (the same team that he helped eliminate in the Europa League qualifiers) on a free transfer, after his loan contract with St Patrick's Athletic expired the previous month.
He won his first piece of silverware with Valletta F.C., when winning the 100th League Anniversary Cup against bitter rivals Floriana on 13 April 2010.
[13] On the opening of the January 2015 transfer window, O'Brien joined NIFL Premiership side and current Irish Cup holders Glenavon on an 18-month deal.
Fabio scored on his Carrick Rangers debut against Ards in a 4–0 win away from home, the club's biggest margin of victory for 3 years.
The former Valletta man then had an unfortunate goal drought of 8 games, however he certainly made up for it when he scored a brace in the 2nd leg of the promotion/relegation playoff final, the first a sensational solo goal and a beautiful panenka penalty to cap off an incredible 4–1 victory for the 'Gers over championship runners-up Institute, sealing a 5-2 aggregate win to stay in the premiership.
On 23 June 2017, it was announced that O'Brien had left Carrick to become player-manager of Leinster Senior League side Verona FC.