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.
In 1959, NCSY hired Rabbi Pinchas Stolper as the first National Director.
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.
During the social upheavals of the 1960s and 1970s, the Orthodox youth of NCSY strove to temper social change through religious tradition. 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. At the 1971 NCSY international convention, delegates passed resolutions in this vein, calling for members to "forge a social revolution with Torah principles."
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".
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.