In 1966, newly elected national president Vincent L. Connery and his supporters defeated a proposed merger into the larger American Federation of Government Employees (AFGE).

The NTEU has been famous for aggressive use of the courts to supplement their statutorily-limited powers to bargain and restraints on traditional labor tactics such as strikes and boycotts.

In 1972, the union sued President Richard M. Nixon, challenging his decision to bypass Congress and postpone salary increases for all federal workers covered by the General Schedule.

It took the issue of the constitutionality of random drug testing of Customs inspectors all the way to the U.S. Supreme Court in NTEU v. Von Raab and it successfully fought initiatives it viewed as anti-worker proposed by the head of the Office of Personnel Management (OPM).

On May 18, 2007, the Federal Labor Relations Authority (FLRA) certified NTEU as the sole representative of some 21,000 bargaining unit employees in the Bureau of Customs and Border Protection (CBP).

The three-member FLRA, which oversees federal sector labor relations, rejected the final appeal of a losing union in a representation election last year covering the CBP workforce.