The league was originally chartered on May 16, 1989 as a men's basketball conference and now sponsors 17 sports (nine for men and 8 for women). The Skyline Conference sponsors baseball, men's and women's basketball, men's and women's cross country, men's golf, men's and women's lacrosse, men's and women's soccer, softball, men's and women's swimming and diving, men's and women's tennis, and men's and women's volleyball.
Primarily comprising schools from the New York metropolitan area, the Skyline Conference currently has 11 full-time member schools, as well as five part-time members that compete in men's lacrosse and men's volleyball only.
Prior to the 2007-08 academic year, the league introduced the Skyline Presidents Cup. St. Joseph's (LI) won the first three Presidents Cups (2007-10), followed by Farmingdale State winning in 2010-11. St. Joseph's (LI) collected its fourth Presidents Cup in 2011-12, with Farmingdale State regaining the title in both 2012-13 and 2013-14.
In May 2018, Manhattanville College announced that they would leave the MAC Freedom Conference and return to the Skyline for the 2019-20 academic year. Manhattanville was a charter member of the Skyline before leaving to join the MAC in 2007. 
|College of Mount Saint Vincent||Riverdale, New York||Dolphins||1847||Private||1,918||1989|
|Farmingdale State College
|East Farmingdale, New York||Rams||1912||Public||8,162||2003|
|Mount Saint Mary College||Newburgh, New York||Knights||1960||Private||2,556||1994|
|Purchase, New York||Panthers||1967||Public||4,379||2007|
|Sarah Lawrence College||Yonkers, New York||Gryphons||1926||Private||1,782||2014|
|St. Joseph's College NY
|Brooklyn, New York||Bears||1916||Private||1,261||2015|
|St. Joseph's College NY
(Long Island Campus)
|Patchogue, New York||Golden Eagles||1978||Private||3,893||1999|
|Throggs Neck, New York||Privateers||1874||Public||1,755||1996|
|College at Old Westbury
|Old Westbury, New York||Panthers||1965||Public||4,364||1989|
|United States Merchant Marine Academy||Kings Point, New York||Mariners||1942||Federal||910||2016[a]|
|Yeshiva University||New York, New York||Maccabees||1886||Private||6,744||1998|
- Merchant Marine had been a charter member in 1989, but left in 2007 to join the Landmark Conference.
|Manhattanville College||Purchase, New York||1841||2019[a]||Private||2,700||Valiants|
- Manhattanville had been a charter member in 1989, but left in 2007 to join the MAC Freedom Conference.
|Institution||Location||Nickname||Founded||Type||Enrollment||Joined||Primary Conference||Skyline Sport|
|Kean University||Union, New Jersey||Cougars||1855||Public||14,404||2006-07||NJAC||men's lacrosse|
|Montclair State University||Montclair, New Jersey||Red Hawks||1908||Public||19,464||2006-07||NJAC||men's lacrosse|
|New Jersey City University||Jersey City, New Jersey||Gothic Knights||1929||Public||8,443||2011-12||NJAC||men's volleyball|
|Stockton University||Pomona, New Jersey||Ospreys||1969||Public||8,458||2006-07||NJAC||men's lacrosse|
|Bard College||Annandale-on-Hudson, New York||Raptors||1860||Private||2007-08||2010-11||Liberty|
|Centenary University||Hackettstown, New Jersey||Cyclones||1867||Private||2003-04||2006-07||CSAC|
|Manhattanville College||Harrison, New York||Valiants||1841||Private||1989-90||2006-07||Freedom|
|Polytechnic Institute of New York University||Brooklyn, New York||Fighting Jays||1854||Private||2007–08||2013–14||dropped athletics|
|The Sage Colleges
Sage College of Albany (men's)
Russell Sage College (women's)
|Albany, New York
Troy, New York
|Stevens Institute of Technology||Hoboken, New Jersey||Ducks||1870||Private||2000-01||2006-07||Empire 8|
(Freedom in 2019)
|Stony Brook University, SUNY||Stony Brook, New York||Patriots[fm 1]||1957||Public||1989-90||1993-94||America East|
(NCAA Division I)
- Stony Brook adopted its current nickname of Seawolves beginning in 1994–95, immediately following the school's departure from the Skyline Conference.
- Stony Brook left while reclassifying to Division I and the America East Conference.
- Manhattanville left to join the Freedom Conference
- Merchant Marine left to join the Landmark Conference and returned in 2016.
- Stevens left to join the Empire 8 Conference
- Centenary (NJ) left to join the Pennsylvania Athletic Conference, now known as the Colonial States Athletic Conference
- Bard left to join the Liberty League
- NYU Poly became affiliated with New York University in 2008, but retained a separate athletic program until it completely merged into NYU in 2014. NYU competes in the University Athletic Association.
- The Kean and Ramapo men's volleyball programs left in 2017 for the Continental Volleyball Conference. Kean remains a men's lacrosse affiliate.
- The Sage Colleges left in 2017 for the Empire 8.
- Manhattanville announced that it will leave the MAC Freedom Conference and rejoin the Skyline for the 2019–20 academic year.
- "Manhattanville to Join Skyline Conference in 2019-20 Academic Year". Skyline Conference. Skyline Conference. Retrieved 11 May 2018.