All lanes of the M62 are now open but police are warning drivers to still expect delays.
The motorcyclist is thought to have suffered serious but not life-threatening injuries.
The motorway was closed eastbound between junction 26 Chain Bar and junction 27 Birstall but one lane has now opened.
Police hope the other lanes will be reopened shortly.
Traffic was queuing beyond junction 24 at Ainley Top and surrounding routes were gridlocked.
Queues have been reported tailing back for 16 miles.
The roads are queueing through Shelf towards the M606 and through Godley in Halifax towards the M62.