[1] Rothfuss started his professional baseball career in 1896 with the Atlantic League's Newark Colts.

[2] That season, he was one of the best hitters in the league, leading the circuit with 26 triples, 13 home runs, and 87 stolen bases.

[8][9][10] He was still suffering from dysentery in May, and in early June, a sportswriter in Kansas City wrote:[11]Johnny Rothfuss ... has shown himself to be the worst type of ingrate.

As soon as the Blues left for the East and Rothfuss was pronounced cured by his physicians he took French leave and nothing has been heard from him since.

The United States Government is warned against accepting this man Rothfuss as a volunteer, for he has certainly shown himself to be the rankest kind of a deserter in the face of duty.

He batted .240 in 27 games, and when Rochester tried to send him to a club in Savannah, Georgia, Rothfuss jumped the team.

[2][14] He played 19 games in the independent Tri-State League in 1906 before applying to the National Board for reinstatement in early 1907.

[14] Rothfuss finished his professional baseball career that year with the Connecticut State League's Hartford Senators.