[6] After practicing law in New York City, he served in the Office of Naval Intelligence from September 1942 to December 1945 obtaining the rank of lieutenant.

He served as staff of the Foreign Affairs Task Force of the Hoover Commission in 1948 before returning to the private sector.

[16][17] In December 1959, when the Port of New York Authority's plans to develop a tract of woodlands and marsh near his estate in Morris County as an international airport serving the New York City region were exposed, Frelinghuysen participated in the opposition by the Jersey Jetport Site Association that was composed of local residents and conservationists,[18][19][20] which raised funds to purchase almost 3,000 acres of the targeted site and donated it to the federal government, to be preserved forever as park lands.

[16][21] In 1966, extortionists targeted Frelinghuysen for blackmail, arranging for him to have a sexual encounter with an underage male and then, posing as police officers, threatening him with public exposure.

[22] He later cooperated with the FBI's investigation of the extortionist ring, but the Justice Department notified the leadership of the House of Representatives and Frelinghuysen was forced off the Armed Services Committee.

[23] After leaving Congress, Frelinghuysen served on the boards of several nonprofit institutions, including the Metropolitan Museum of Art and the New York Botanical Garden.