Attempts to encourage more people to use the service, and efforts to find funding to keep it going, have failed.
The shuttle bus was free until last summer, when health organisations said they could no longer afford to fund the service.
East Riding of Yorkshire Council stepped in to save it, and Scarborough and Ryedale Clinical Commissioning Group, York Teaching Hospital NHS Foundation Trust and Bridlington Town Council all give financial backing.
Passengers were charged £5 for a return journey but numbers have not increased enough to make it viable.
A second 12-week pilot scheme ends on Sunday, January 29.
Cllr Andy Burton, East Riding of Yorkshire Council’s portfolio holder for planning, highways and transportation, said: “Our trial shuttle bus was used by passengers and people found it very useful, but unfortunately it was only covering just over a third of its overall costs.
“We extended the trial to give it another chance, and the other partners made a contribution to costs and helped us advertise the service, but unfortunately the service has come nowhere near to being self-financing”.
The trial shuttle bus was operated by North Holderness Community Transport (HART) six times a day between the two hospital sites.
The service typically carried around 140 passengers per week, mainly return journeys, but would need to attract around 350 return passengers a week to cover its costs.
The original shuttle bus service was first launched in 2008 by the Scarborough and North East Yorkshire NHS Healthcare Trust after acute medical services were transferred from Bridlington Hospital to Scarborough Hospital.
As an alternative Bridlington residents can travel by rail or the EYMS 121 bus service to Scarborough Rail Station and connect with EYMS service 10 to Scarborough Hospital.
The 121 bus services run hourly and rail services operate approximately every hour-and-a-half.
Details are available on the EYMS website www.eyms.co.uk or from Busline 01482 592929.
Rail information can be found at www.nationalrail.co.uk or by calling 03457 484950.