On 31 December 2012, O'Toole signed for League Two team Bristol Rovers, initially on a one-month deal.
The move saw him link up with former Colchester manager John Ward, who had recently joined Rovers.
He made his debut the following day in a 2–1 win over Plymouth Argyle.
He scored his first goal for the club in a convincing 3–0 away win over Fleetwood Town on 12 January 2013 with an 18-yard strike to seal the win.
He also scored in another 3–0 emphatic victory over Burton Albion on 2 March 2013, scoring from close-range.
In his final game of his loan spell, he scored the opening goal in a 4–2 away victory over Dagenham & Redbridge.
O'Toole made 18 appearances alongside scoring his three goals for the club in a loan that was eventually extended until 1 April 2013.
Manager Ward expressed interest in signing him permanently over the summer, with O'Toole still having one year to run on his Colchester contract.

After a long protracted transfer saga, O'Toole signed a three-year contract with Bristol Rovers, joining for an undisclosed fee on 24 July 2013.
The season proved to be bittersweet for O'Toole.
He ended the season as Rovers' top scorer with 15 goals and was included in the PFA Team of the Year for League Two but Rovers' suffered relegation out of the Football League for the first time since their admission in 1920.
This was followed by O'Toole activating his release clause with Rovers leaving him free to join a new club on 30 May 2014.
On 31 December 2012, O'Toole signed for League Two team Bristol Rovers, initially on a one-month deal. The move saw him link up with former Colchester manager John Ward, who had recently joined Rovers. He made his debut the following day in a 2–1 win over Plymouth Argyle. He scored his first goal for the club in a convincing 3–0 away win over Fleetwood Town on 12 January 2013 with an 18-yard strike to seal the win. He also scored in another 3–0 emphatic victory over Burton Albion on 2 March 2013, scoring from close-range. In his final game of his loan spell, he scored the opening goal in a 4–2 away victory over Dagenham & Redbridge. O'Toole made 18 appearances alongside scoring his three goals for the club in a loan that was eventually extended until 1 April 2013. Manager Ward expressed interest in signing him permanently over the summer, with O'Toole still having one year to run on his Colchester contract.
After a long protracted transfer saga, O'Toole signed a three-year contract with Bristol Rovers, joining for an undisclosed fee on 24 July 2013. The season proved to be bittersweet for O'Toole. He ended the season as Rovers' top scorer with 15 goals and was included in the PFA Team of the Year for League Two but Rovers' suffered relegation out of the Football League for the first time since their admission in 1920. This was followed by O'Toole activating his release clause with Rovers leaving him free to join a new club on 30 May 2014.
John-Joe O'Toole