In 2007, Hynes began his professional career with the Class A Short-SeasonEugene Emeralds of the Northwest League. He had a 3–2 record with a 1.54 ERA, four saves, and 50 strikeouts in 41 innings pitched. His 30 games were all in relief. Hynes was promoted to the Class-A Fort Wayne Wizards of the Midwest League in 2008. He went 0–2 with a 4.60 ERA and 38 strikeouts in 32 games. In 2009, Hynes split the season between the Class A Fort Wayne Wizards and the Class A-Advanced Lake Elsinore Storm of the California League. He put together a 2–0 record with a 1.62 ERA in 13 games with Fort Wayne before his promotion to Lake Elsinore. With the Storm, he went 3–3 with a 2.90 ERA giving him a combined record of 5–3 with a 2.62 ERA, two saves, and 61 strikeouts in 75 innings pitched. Hynes made his MLB debut with the Padres on July 14, 2013, pitching the ninth inning of a 10–1 victory against the San Francisco Giants. He appeared in six games for the Padres and was 1–1 with an 11.12 ERA in 5 innings. He was designated for assignment on October 25, 2013.
He was traded to the Cleveland Indians for cash considerations on October 31, 2013. They designated him for assignment on March 30, 2014, and he was traded to the Los Angeles Dodgers for Duke von Schamann on April 6. He was assigned to the Triple-AAlbuquerque Isotopes. The Dodgers designated him for assignment on August 10.
On August 13, 2014, Hynes was claimed off waivers by the Toronto Blue Jays and assigned to the Triple-A Buffalo Bisons. He was invited to 2015 spring training, and pitched 12 shutout innings allowing only 3 hits and 2 walks, while striking out 11. His strong performance earned him a role in the bullpen to open the 2015 season. He was optioned Buffalo on April 19. On September 1, Hynes was designated for assignment. He elected free agency on November 6. On February 12, 2016, Hynes agreed to a minor league contract with the Blue Jays. He started the season with the Double-A New Hampshire Fisher Cats, was promoted to the Buffalo Bisons on April 23, and returned to New Hampshire on April 25.
Cleveland Indians
On August 4, 2016, Hynes signed a minor league contract with the Cleveland Indians and was assigned to the Triple-A Columbus Clippers.
Hynes signed a minor league contract with the Dodgers in February 2017. They assigned him to the Double-A Tulsa Drillers of the Texas League to start the 2017 season. He appeared in 23 games for Tulsa and additional three games for the Oklahoma City Dodgers and was 6–1 with a 3.90 ERA between the two teams. On November 3, 2017, Hynes resigned a minor league deal with the Dodgers, however he was released on February 14, 2018.
Retirement
On March 10, 2018, Hynes retired from baseball to join the Dodgers' front office as a minor league rehabilitation coordinator.