The service will stop on January 27 and passengers booked on flights after that date will be transferred to other airlines.
A spokesman for parent company Virgin Atlantic said: "We support Virgin Nigeria's decision to focus on its profitable domestic and regional operations and believe it can be even more successful as a result.”
Virgin Nigeria currently operates six flights a week between London Gatwick and Lagos as well as a weekly service from London Heathrow. Virgin Atlantic’s daily Lagos flights from Heathrow will remain unaffected.