#Series cancelled due to heavy rain. Auburn and Oneonta declared co-champions.
*Series cancelled due to September 11, 2001, terrorist attacks. Brooklyn and Williamsport declared co-champions.
| New York-Penn League Champions |
| Year |
Winner |
| 1939 |
Olean Oilers |
| 1940 |
Olean Oilers |
| 1941 |
Bradford Bees |
| 1942 |
Jamestown Falcons |
| 1943 |
Wellsville Yankees |
| 1944 |
Jamestown Falcons |
| 1945 |
Batavia Clippers |
| 1946 |
Batavia Clippers |
| 1947 |
Jamestown Falcons |
| 1948 |
Lockport Reds |
| 1949 |
Bradford Blue Wings |
| 1950 |
Olean Oilers |
| 1951 |
Hornell Dodgers |
| 1952 |
Jamestown Falcons |
| 1953 |
Jamestown Falcons |
| 1954 |
Corning Red Sox |
| 1955 |
Hamilton Cardinals |
| 1956 |
Wellsville Braves |
| 1957 |
Erie Sailors |
| 1958 |
Geneva Redlegs |
| 1959 |
Wellsville Braves |
| 1960 |
Wellsville Braves |
| 1961 |
Olean Red Sox |
| 1962 |
Auburn Mets |
| 1963 |
Batavia Pirates |
| 1964 |
Auburn Mets |
| 1965 |
Binghamton Triplets |
| 1966 |
Auburn Mets |
| 1967 |
Auburn Twins |
| 1968 |
Oneonta Yankees |
| 1969 |
Oneonta Yankees |
| 1970 |
Auburn Twins |
| 1971 |
Oneonta Yankees |
| 1972 |
Niagara Falls Pirates |
| 1973 |
Auburn Phillies |
| 1974 |
Oneonta Yankees |
| 1975 |
Newark Co-Pilots |
| 1976 |
Elmira Red Sox |
| 1977 |
Oneonta Yankees |
| 1978 |
Geneva Cubs |
| 1979 |
Oneonta Yankees |
| 1980 |
Oneonta Yankees |
| 1981 |
Oneonta Yankees |
| 1982 |
Niagara Falls Sox |
| 1983 |
Utica Blue Sox |
| 1984 |
Little Falls Mets |
| 1985 |
Oneonta Yankees |
| 1986 |
St. Catharines Blue Jays |
| 1987 |
Geneva Cubs |
| 1988 |
Oneonta Yankees |
| 1989 |
Jamestown Expos |
| 1990 |
Oneonta Yankees |
| 1991 |
Jamestown Expos |
| 1992 |
Geneva Cubs |
| 1993 |
Niagara Falls Rapids |
| 1994 |
New Jersey Cardinals |
| 1995 |
Watertown Indians |
| 1996 |
Vermont Expos |
| 1997 |
Pittsfield Mets |
| #1998 |
Auburn Doubledays |
| #1998 |
Oneonta Yankees |
| 1999 |
Hudson Valley Renegades |
| 2000 |
Staten Island Yankees |
| *2001 |
Brooklyn Cyclones |
| *2001 |
Williamsport Crosscutters |
| 2002 |
Staten Island Yankees |
| 2003 |
Williamsport Crosscutters |
| 2004 |
Mahoning Valley Scrappers |
| 2005 |
Staten Island Yankees |
| 2006 |
Staten Island Yankees |
| 2007 |
Auburn Doubledays |
