About 40 minutes into the flight to New York on Monday, the two pilots became aware of the “rostering error”, the airline said.
Flight VS3 had reached the skies over Ireland before returning to Heathrow.
Virgin Atlantic said a replacement for the first officer was found and the plane departed again for New York.
The airline insisted safety was not compromised and explained the initial first officer joined Virgin Atlantic in 2017.
He was fully qualified under UK aviation regulations, the airline added, but had not completed a final assessment flight that was part of the airline’s internal requirements.
The flight turned back as the captain had not been designated as a trainer.
Control of an aircraft is usually shared between a first officer and the captain, but the latter holds ultimate responsibility for what happens on a flight.
A Virgin Atlantic spokeswoman said: “The qualified first officer, who was flying alongside an experienced captain, was replaced with a new pilot to ensure full compliance with Virgin Atlantic’s training protocols, which exceed industry standards.
“We apologise for any inconvenience caused to our customers, who arrived two hours and 40 minutes later than scheduled as a result of the crew change.”
A Civil Aviation Authority (CAA) spokesperson confirmed both pilots were suitably licensed and “qualified to undertake the flight”.