Wagner was born in Harlem, New York, in September 1880. He began his baseball career playing for the Waverly Club in the New York State League in 1901. In 1902, he began the season playing for Columbus in the American Association, and played briefly in 17 games for the New York Giants of the National League. He spent the remainder of the 1902 season with the Newark Sailors and continued to play for the Eastern League team through 1906.In 1906, Wagner joined the Boston Red Sox. He played for the Red Sox from 1906 to 1918, missing only the 1914 and 1917 seasons. He was the captain of Boston's 1912 World Series championship team. He also played for the Red Sox World Series championship teams in 1915, 1916 and 1918. Wagner and Harry Hooper were the only players to play on all four of the Red Sox World Series championship teams.
Wagner was considered to be a valuable infielder while playing with the Red Sox and was reputed to have "an exceptionally powerful and accurate throw." He was also known to block the basepaths with his "exceptionally big" feet. With 141 career stolen bases for the Red Sox, Wagner ranked third in team history when he retired (trailing Hall of Famers Harry Hooper and Tris Speaker) and still ranks fifth on the all-time Red Sox stolen base list.
After being released by the Red Sox in January 1916, Wagner served as the player-manager of the Hartford team in the Eastern League for the first part of the 1916 season. He returned to the Red Sox in late June 1916.
In 1920, Wagner closed out his playing career as the player-manager of the Norfolk Mary Janes in the Virginia League.
After seven years out of baseball, Wagner was hired as a coach for the Boston Red Sox under Bill Carrigan. He was reported to be Carrigan's "right hand man" during the 1928, 1929, and 1930 seasons. In 1930, he was hired as manager of the Red Sox after Carrigan retired. In Wagner's sole season as manager, the Red Sox finished last in the American League with a 52-102 (.338) record. On September 29, 1930, Wagner's resignation as manager of the Red Sox was accepted by team president Bob Quinn. He never managed again.
After retiring from baseball, Wagner worked as the superintendent of a lumber yard in New Rochelle, New York. He also coached the baseball teams of the New Rochelle Police and Fire Departments and Elks Club.
Wagner was married to Martha Hahn Wagner. They had two sons and four daughters. In March 1943, Wagner died of a heart ailment at his home on Van Guilder Avenue in New Rochelle at age 62.