Washington State Ferries says the Elwha has been repaired and should resume service Monday after a Coast Guard inspection.
Hundreds of passengers were told to put on life jackets Sunday because of smoke from the engine room.
Ferries spokeswoman Marta Coursey says it was a precaution on the side of safety while the crew made certain there was no serious fire threat from an electronic component failure in the propulsion control system.
The ferry from Friday Harbor was able to make it to Anacortes at a reduced speed.
Some San Juan Islands runs were cancelled or delayed Monday morning because of the Elwha problem.
Washington State Ferries also canceled or delayed some routes last week as it shuffled vessels when two other ferries needed unexpected repairs.