The Welsh Air Ambulance was called after the man sustained serious injuries in a collision with a car at about 14:45 GMT on Wednesday.
The A465 between the A4059 Hirwaun Road and A4061 Rhigos Road roundabouts was initially closed in both directions.
The westbound carriageway has now reopened.
Motorists are advised to avoid the area as police warn of long tailbacks.
The eastbound carriageway remains closed as South Wales Police investigate the incident.
Traffic is being diverted through Aberdare and Hirwaun village,
A cyclist has been airlifted to hospital after an accident that closed the Heads of the Valleys road near Hirwaun.