Born in Central City, Nebraska, Wagner's career in professional baseball began at a young age.

In 1947, only 19 and fresh out of the Navy, he took a position as business manager of a Class D Georgia–Florida League team, a Detroit Tigers affiliate.

He held minor league administrative posts in Flint, Michigan; Miami, Florida; San Antonio, Texas; Hutchinson, Kansas; and Lincoln, Nebraska.

He spent the next fifteen years in the front office during that team's successful run as "The Big Red Machine", beginning by supervising business affairs for the Reds, helping to pioneer, develop and refine marketing and promotional efforts that resulted in a series of attendance records while soon being called Howsam's “hatchet man".

Wagner innovated the practice of Major League teams wearing green-trimmed uniforms on March 17 in honor of St. Patrick's Day.

Wagner continued as president and general manager until he was fired by the Reds on July 11, 1983 by owners James and Bill Williams, who replaced him with Bob Howsam on an interim basis.

In 1986, various players would come through in free agency or in trades, such as Larry Andersen or Danny Darwin; both would play four years with the team, and while Andersen would later be part of a future legendary trade made by the Astros, Darwin never saw action as a postseason starter because he was being saved for a World Series bid (due to the Astros relying on a three-man trio of starters).

Wagner stated that a lack of understanding over what team owner John McMullen wanted from him was a key factor.

He served as a top-level aide for several years, and he ran the New York staff for a time when Bud Selig took over as commissioner in 1993.