For their first few seasons NYCFC affiliated with Wilmington Hammerheads FC[1] and then with San Antonio FC[2] but these partnerships were little used and the club continued with no minor league affiliate for several seasons afterwards.

It would be placed in the third tier of the United States soccer league system below the USL Championship, which had previously hosted affiliated and reserve teams.

[4] On February 24, 2022, it was announced that NYCFC II would play its home matches at Belson Stadium on the campus of St. John's University.

[7] On July 15, 2024, NYCFC II announced that would play a portion of its schedule at Icahn Stadium on on Randalls Island in Manhattan.

[8] The club made a $3 million donation to fund upgrades to bring the pitch up to professional soccer standards.