Currently, Elmira Pioneers play as members of the Perfect Game Collegiate Baseball League (PGCBL).

The Pioneers name first appeared in 1900, when the team joined a new New York State League that was founded a year earlier.

The Elmira Red Jackets, presumably named after the Seneca chief, were charter members of the new New York–Penn League in 1923.

Armando Marsans, one of the first two Cubans to play Major League Baseball, served as their manager in 1923.

After winning the league championship that year, they signed on with the Brooklyn Dodgers and re-established the Colonels name for the 1937 season, in which they repeated as champions.

Elmira did not field a team in 1956, but joined the Class-A short-season New York–Penn League in 1957 as a Washington Senators affiliate.

Two highlights of their time with the Phillies were Jim Guinn's 33-game hitting streak in 1959, and Vern Kemp striking out 21 batters in a single game during 1961.

The New York–Penn League affiliate of the Boston Red Sox moved from Williamsport, Pennsylvania, to Elmira for the 1973 season, and remained there through 1992.

After some significant scrambling, an ownership group anchored by an Elmira native living in Maryland, John Ervin, got a new Pioneers team into the independent Northeast League before the 1996 season began.