The 40-year-old from Dungannon was involved in an incident in the Supertwins race at the fast right-hander on the uphill run past the Dhu Varren railway bridge in Portrush on Thursday evening.
Farquhar sustained chest and pelvic injuries and was transported to hospital by a PSNI helicopter.
Gloucestershire’s Dan Cooper was also caught up in the crash as he battled with Farquhar for the lead and sustained a shoulder injury. The 28-year-old has been discharged from the Causeway Hospital in Coleraine.
On Friday morning, a statement from the NW200 organisers said: “Ryan Farquhar was taken by airmed to the Royal Victoria Hospital, Belfast with chest and pelvic injuries. Ryan remains seriously ill in intensive care following surgery.”
Castledawson’s Nico Mawhinney, who crashed during Superbike qualifying on Thursday, is in a stable condition at the Royal Victoria Hospital and has been admitted to a ward.
The former Irish Superbike champion, who was making his debut at the event, came off at the Mill Road roundabout in Portstewart.