Moylan was signed by the Atlanta Braves in 2006 and assigned to their Triple-A Richmond club.
On 11 April 2006, Moylan was called up to the Braves to replace Joey Devine in the bullpen and he made his MLB debut the following day, pitching one scoreless inning against the Philadelphia Phillies; however he was later sent back to the Richmond club.
He pitched in 15 total games during three separate call-ups in 2006, with a 4.80 ERA in 15 innings.

At the end of spring training in 2007, Moylan was again assigned to Richmond, but he was quickly called up on 14 April due to the injury of pitcher Chad Paronto.
Moylan sealed a permanent spot on the roster as he proved invaluable to the Braves bullpen in 2007.
Moylan earned his first major league win against the Florida Marlins in Miami on 24 April 2007.
He earned his first major league save three days later against the Colorado Rockies in Denver.
He finished the season 5–3 with a 1.80 ERA.
 He led the majors in intentional walks allowed, with 12.

In April 2008, The Braves placed Moylan on the 15-day disabled list with a sore right elbow.
Medical examination showed the ulna collateral ligament in Moylan's right elbow was compromised by a bone spur.
On 5 May, Moylan was transferred to the 60-day disabled list, and missed the remainder of the 2008 season recovering from Tommy John surgery.

Moylan exceeded rehabilitation expectations and was declared fit to pitch during the Braves' 2009 Spring Training camp in Orlando, Florida.
Moylan worked with former Braves closer Gene Garber to work on his side-arm/submarine delivery.
He used the spring work to continue to gain arm strength, and began the season on the Braves active roster.
 After a few shaky appearances in April, Moylan began to find more consistency during May, settling into his role as the team's primary 7th inning specialist.
Between the 80 appearances he made in 2007 and the 87 appearances in 2009, he became the first Braves pitcher to have two seasons with 80 or more games pitched.
In addition he did not allow a home run in 2009, setting a Major League Baseball record for the most consecutive appearances to start a season without giving up a home run, eclipsing the record of 73 set by Brian Shouse with the Milwaukee Brewers in 2007.

Moylan appeared in 85 games for the Braves in 2010, finishing with a 6–2 record and a 2.97 ERA.
In 2011, Moylan appeared in seven games before being placed on the disabled list in mid-April.
He underwent successful back surgery on 17 May 2011, and was expected to miss at least two months.
Moylan returned to the Braves on 3 September 2011, but after six appearances, he was diagnosed with torn rotator cuff and labrum in his pitching shoulder.
Although he was initially expected to miss most or possibly all of 2012, it was later estimated that he would need six-month recovery period, allowing him to be ready for spring training in 2012.

While with the Braves, Moylan gained a reputation as a fan favorite through his embrace of Twitter  and his sense of humor, even posting a link to a photo of himself in a dress stating he was wearing it to the ESPYs.

On 17 January 2012, the Braves re-signed Moylan to a minor-league deal worth approximately $1 million.
He only appeared in eight games with the Braves in 2012.
Moylan was signed by the Atlanta Braves in 2006 and assigned to their Triple-A Richmond club. On 11 April 2006, Moylan was called up to the Braves to replace Joey Devine in the bullpen and he made his MLB debut the following day, pitching one scoreless inning against the Philadelphia Phillies; however he was later sent back to the Richmond club. He pitched in 15 total games during three separate call-ups in 2006, with a 4.80 ERA in 15 innings.
At the end of spring training in 2007, Moylan was again assigned to Richmond, but he was quickly called up on 14 April due to the injury of pitcher Chad Paronto. Moylan sealed a permanent spot on the roster as he proved invaluable to the Braves bullpen in 2007. Moylan earned his first major league win against the Florida Marlins in Miami on 24 April 2007. He earned his first major league save three days later against the Colorado Rockies in Denver. He finished the season 5–3 with a 1.80 ERA.  He led the majors in intentional walks allowed, with 12.
In April 2008, The Braves placed Moylan on the 15-day disabled list with a sore right elbow. Medical examination showed the ulna collateral ligament in Moylan's right elbow was compromised by a bone spur. On 5 May, Moylan was transferred to the 60-day disabled list, and missed the remainder of the 2008 season recovering from Tommy John surgery.
Moylan exceeded rehabilitation expectations and was declared fit to pitch during the Braves' 2009 Spring Training camp in Orlando, Florida. Moylan worked with former Braves closer Gene Garber to work on his side-arm/submarine delivery. He used the spring work to continue to gain arm strength, and began the season on the Braves active roster.  After a few shaky appearances in April, Moylan began to find more consistency during May, settling into his role as the team's primary 7th inning specialist. Between the 80 appearances he made in 2007 and the 87 appearances in 2009, he became the first Braves pitcher to have two seasons with 80 or more games pitched. In addition he did not allow a home run in 2009, setting a Major League Baseball record for the most consecutive appearances to start a season without giving up a home run, eclipsing the record of 73 set by Brian Shouse with the Milwaukee Brewers in 2007.
Moylan appeared in 85 games for the Braves in 2010, finishing with a 6–2 record and a 2.97 ERA. In 2011, Moylan appeared in seven games before being placed on the disabled list in mid-April. He underwent successful back surgery on 17 May 2011, and was expected to miss at least two months. Moylan returned to the Braves on 3 September 2011, but after six appearances, he was diagnosed with torn rotator cuff and labrum in his pitching shoulder. Although he was initially expected to miss most or possibly all of 2012, it was later estimated that he would need six-month recovery period, allowing him to be ready for spring training in 2012.
While with the Braves, Moylan gained a reputation as a fan favorite through his embrace of Twitter  and his sense of humor, even posting a link to a photo of himself in a dress stating he was wearing it to the ESPYs.
On 17 January 2012, the Braves re-signed Moylan to a minor-league deal worth approximately $1 million. He only appeared in eight games with the Braves in 2012.
Peter Moylan