Wohlers, a native of Holyoke, Massachusetts, was drafted in the eighth round of the 1988 amateur draft by the Atlanta Braves. He went on to make his major league debut with the organization on August 17, 1991. Less than a month later, on September 11, 1991, Wohlers teamed with fellow Braves hurlers Kent Mercker and Alejandro Pena for a combined no-hitter against the San Diego Padres; Wohlers pitched two innings in relief of Mercker.

After spending the following three seasons as a setup pitcher, Wohlers was given the job as a closer in 1995. He went on to record 97 saves over the next three seasons, including the clinching Game 6 of the 1995 World Series, establishing himself as one of the best closers in the majors.

Wohlers' success would not last forever. In Game 4 of the 1996 World Series, Wohlers gave up a stunning 3-run homerun to Jim Leyritz that tied the game 6-6. After this, the momentum of the Series shifted and the Yankees won it in six games. Many observe that Wohlers was never the same after that. In 1998, Wohlers seemed to lose all ability to control his pitches. He spent part of the season at AAA Richmond, but he still finished the season with a major league ERA of 10.18. His control problems were dramatic. In 20.1 major league innings Wohlers walked 33 batters. After being sent down to AAA, Wohlers walked 36 batters in only 12.1 innings. His symptoms were a prime example of what is commonly known as Steve Blass disease - a psychological block which manifests itself when baseball players overthink the act of throwing a baseball and consequentially become unable to pitch with any sort of control.

He began the following season in a similar fashion: in two outings he recorded an ERA of 27.27 in 0.2 innings pitched with 6 walks. The Atlanta faithful, although frustrated with Wohlers' seemingly constant fastballs to the backstop or behind batters, rallied behind the embattled pitcher and would fervently cheer him on whenever he was in the game. After being recalled from Richmond, he entered a game and recorded a strikeout, his first in months, and received a rousing standing ovation from the crowd at Turner Field.

On April 16, 1999, the Braves traded Wohlers to the Cincinnati Reds in return for John Hudek. The day after signing for the Reds he was put on the disabled list with an anxiety disorder. While undergoing treatment for his anxiety, Wohlers had Tommy John surgery on his elbow which ended his season. Wohlers returned to baseball for the 2000 season in his old role as a setup man. He split the following season between the Reds and the New York Yankees before being traded to the Cleveland Indians prior to the 2002 season.

In his first season with the Indians, Wohlers recorded an ERA of 4.79, with seven saves, three wins, four losses, and a much improved walk ratio. After experiencing pain in his right elbow in spring training before the 2003 season Wohlers had an operation to remove several bone chips, ruling him out for the first two months of the season. Unfortunately his season was ended in the second game of his rehabilitation assignment at AA Akron when he ruptered the tendon graft he had had in his elbow in 1999. He had Tommy John surgery for the second time in August of that year, which should have allowed him to return for the 2004 season. However, Wohlers decided not to return due to personal reasons and was released by the Indians. He has not returned to baseball, although he also has not formally announced his retirement. His career record is 39-29 with an ERA of 3.97 and 119 saves.