On May 19, 2011, Morales was acquired by the Boston Red Sox for a player to be named later or cash considerations.
On May 22, he made his debut appearance for the Red Sox in a game against the Chicago Cubs.
Morales finished the 2011 season with Boston making 36 relief appearances going 1-1 with a 3.62 ERA.
Overall in 2011 combined with two teams, Morales made a total of 50 appearances going 1-2 with a 3.69 ERA.

Near the end of the 2012 season, Morales was injured.
He was diagnosed with a shoulder injury.
He had a starting job before September and stuck with it until his injury.
On January 16, 2012, Morales signed a one-year deal worth $850K with the Red Sox, avoiding arbitration.
During the 2012 season, Morales made 37 appearances (9 starts) going 3-4 with a 3.77 ERA.
In the off-season he trained to be a starter for 2013.

In 2013, Morales made 20 appearances (1 start) going 2-2 with a 4.62 ERA.
Morales made 3 appearances in the postseason.
In his final appearance in a Red Sox uniform, he relieved Clay Buchholz in Game 6 of the ALCS.
With the Red Sox ahead 1-0 in the 6th inning and two inherited runners on base, Morales walked Prince Fielder on 4 pitches, then fell behind Victor Martinez before yielding a 2-run Wall Ball single.
Morales was replaced by Brandon Workman who ended the inning without further damage.
The Sox won the game when Shane Victorino hit a 7th inning grand slam.
Morales did not pitch in the World Series as the Red Sox won the championship over the St. Louis Cardinals.
He was traded by the Red Sox before the end of the year.
On May 19, 2011, Morales was acquired by the Boston Red Sox for a player to be named later or cash considerations. On May 22, he made his debut appearance for the Red Sox in a game against the Chicago Cubs. Morales finished the 2011 season with Boston making 36 relief appearances going 1-1 with a 3.62 ERA. Overall in 2011 combined with two teams, Morales made a total of 50 appearances going 1-2 with a 3.69 ERA.
Near the end of the 2012 season, Morales was injured. He was diagnosed with a shoulder injury. He had a starting job before September and stuck with it until his injury. On January 16, 2012, Morales signed a one-year deal worth $850K with the Red Sox, avoiding arbitration. During the 2012 season, Morales made 37 appearances (9 starts) going 3-4 with a 3.77 ERA. In the off-season he trained to be a starter for 2013.
In 2013, Morales made 20 appearances (1 start) going 2-2 with a 4.62 ERA. Morales made 3 appearances in the postseason. In his final appearance in a Red Sox uniform, he relieved Clay Buchholz in Game 6 of the ALCS. With the Red Sox ahead 1-0 in the 6th inning and two inherited runners on base, Morales walked Prince Fielder on 4 pitches, then fell behind Victor Martinez before yielding a 2-run Wall Ball single. Morales was replaced by Brandon Workman who ended the inning without further damage. The Sox won the game when Shane Victorino hit a 7th inning grand slam. Morales did not pitch in the World Series as the Red Sox won the championship over the St. Louis Cardinals. He was traded by the Red Sox before the end of the year.
Franklin Morales