After completing his secondary education, Sockalexis began his college career in 1894 at the College of the Holy Cross. While there, he participated on the school's baseball, football, and track teams. Sockalexis spent those summers playing baseball in the Trolley League along the coast of Maine. After the end of the 1895-96 baseball season, the Holy Cross baseball coach accepted a position at the University of Notre Dame in February 1897. When that happened, Sockalexis decided to transfer to Notre Dame. In his two seasons at Holy Cross, Sockalexis compiled a .444 batting average.