It will still offer customers Saudi flight bookings via a codeshare with partner airline Saudia.
Saudia offers flights to Riyadh and Jeddah from London and from Manchester to Jeddah.
The airline will shift capacity to other routes in Asia and the Americas.
“We are very sorry for the disappointment this change will cause. We know this route has been important to many of our customers, and we’re truly grateful for their support,” said CCO Dave Geer.
“We’re pleased to be offering increased flying to our three largest markets – the USA, Caribbean and India – to help meet this demand.
Virgin will almost double the number of flights to Bengaluru, India this summer and deploy larger aircraft to Mumbai.
It is also offering more Jamaica flights this summer.
Virgin customers booked to Riyadh will be notified and given the option of rebooking with another airline or receiving a refund.