Though outreach to public school youth was started by Chabad in the 1930s, the Torah Leadership Seminar, created in 1954 by DCS of Yeshiva University under Dr Abraham Stern, developed the Shabbaton model (for more details see Baal teshuva). There was a core of NCSY from two early founded regions Midwest Region (founded 1951) and Southern Region (founded in 1952 by Rabbi Abraham Isaac Rosenberg and Mr. Abe Rabhan of B’nai B’rith Jacob synagogue in Savannah, Georgia). In 1954, Harold and Enid Boxer donated the money to create a national organization from the already-existing Southern and Midwest Regions.^[5]

In 1959, NCSY hired Rabbi Pinchas Stolper as the first National Director.^[6]

In the 1960's there was an emphasis on NCSY Publications with many volumes written by Pinchas Stopler and then later the Aryeh Kaplan Series.They also put out the NCSY Guide to Blessings and the NCSY Bencher.^[7]

During the social upheavals of the 1960s and 1970s, the Orthodox youth of NCSY strove to temper social change through religious tradition.^[8] In this period, at least one NCSY chapter took public action on this point, passing a resolution rejecting marijuana and other drugs as a violation of Jewish law.^[8] At the 1971 NCSY international convention, delegates passed resolutions in this vein, calling for members to "forge a social revolution with Torah principles."^[8]

In the mid 1970s, NCSY started a boys camp at Ner Israel Rabbinical College in Baltimore, MD. It was originally known as "NCSY Goes to Yeshiva," and later changed it name to "Camp NCSY Sports".^[9]

In 1970, the Israel Summer Institute for Jewish teens was founded. Rabbi Stolper assisted NCSY in expanding internationally into Canada, Israel, Australia, Chile, and Ukraine.

In 2007, NCSY launched a sexual abstinence campaign.^[10]

The organization has produced many Jewish children's entertainers who have remained in outreach work, including Uncle Moishy and the Mitzvah Men and Zale Newman.

According to the Orthodox sociologist Chaim Waxman, there has been an increase in Haredi influence on NCSY.^[11] Waxman based this on NCSY's own sociological self-study.^[12]

NCSY is divided into geographic regions throughout North America. They are New England, Upper New York, New York-Long Island, New Jersey, Atlantic Seaboard, Central East, Southern, South Florida, Greater Midwest, Southwest, West Coast, Northwest, and Canada. Additionally, NCSY runs programming branches in Israel and now Chile and Germany. Each Region is divided into chapters. A chapter is typically a city, or a group of surrounding towns. In heavily populated Jewish areas like New Jersey, counties may have several chapters.

Many chapters in NCSY appoint or elect a group of NCSYers to serve on a chapter board,who work with the advisors or city directors to assist with programming or outreach. Many regions do the same thing, and have a regional board, who do similar things for the region. The International Board consists of representatives from many different regions.

NCSY's programming is divided into two age groups, "junior" and "senior"; these generally encompass 5th–8th grades and 9th–12th grades, respectively. Some programs span both age groups, but most programming is unique for each.

Currently, while on Shabbatons kids are treated to skits, learning sessions and ebbing, where participants sit in a circle around the "circle guy" where they sing songs and do funny routines. They are housed either in hotels, or grouped with sponsor families who take them in for the weekend.