Flights were prevented from taking off for more than an hour due to "automation issues," the Federal Aviation Administration said in an initial notice.
United Airlines confirmed on its Twitter account that it experienced a "network connectivity issue" and apologized to customers "for any inconvenience."
Wednesday's delay began at 8:26 am EST (1226 GMT) and initially applied to all flights operated by United and its subcontractors. While the subcontractors were soon cleared, United was unable to fix the problem for their entire service until 1347 GMT.
In early June, United flights were grounded in the US for more than 40 minutes due to a computer problem.
Long lines at check-in and confused, frustrated customers were seen on local television stations as a reported 3,500 flights worldwide were affected.
An AFP reporter at the Newark, New Jersey airport said things were calm inside the terminal where people had already checked in for their flights.
United, owned by parent