United said it had suffered a "network connectivity" problem - the same issue that grounded its flights on 2 June.
The US aviation authority (FAA) said the airline resolved the issues at about 10:00 ET (14:00 GMT).
The company has suffered technical issues in the past, including one that meant first-class seats were sold in error for just $100 (Â£65) in February.
"We experienced a network connectivity issue this morning. We are working to resolve this and apologise to our customers for any inconvenience," United said in a statement.
The problem impacted as many as 3,500 flights, the airline told the CNBC TV news network.
United customers complained of delays and a lack of information on Twitter on Wednesday morning.
One passenger, Jeralyn Novak, tweeted: "Never flying @united ever again! The whole computer system is down and stuck in Boise."
Betsy Fischer Martin, a journalist travelling with United, tweeted: "Our @united airlines pilot on their global outage: "It's like someone pulled the plug on our computers - It's embarrassing, I apologise.""
United said it was "recovering" and "restoring flight ops" after the FAA order was lifted, but long queues were reported at airports across the US.
It was the latest in a series of technical problems that the US carrier has had in recent months.
Last month, United was again forced to ground its planes across the US due to an unspecified computer problem.
And in February, the company cancelled thousands of bookings after a computer glitch allowed transatlantic flights to be bought for very low prices.
United said it would not honour the fares as the error was caused by a "third party software provider" - provoking criticism from customers.
It is not the only airline to have suffered with technical issues though.
In April, rival US carrier American Airlines also had to ground its planes after a glitch caused iPad software - used by its pilots to view flight plans - to stop working.
US carrier United Airlines grounded all of its flights for about two hours on Wednesday due to a technical issue.