The train will run twice a day on the 84-mile round trip between Fort William and Mallaig which takes in the spectacular Glenfinnan Viaduct on what has been voted the greatest railway journey.
Several of the vintage red carriages, which date back to the 1950s, featured in the Potter films.
A West Coast Railways spokesman said: “It’s wonderful to be back – even if we are a little late. But we are looking forward to a great summer season.
“People are desperate to get out again after the lockdown and the roll-out of the Covid vaccine has been a real shot in the arm for us.
“But the safety of passengers, staff and local people are still paramount to us. So some things will be a little different this summer.”
Crowds of railway enthusiasts turned out last week to watch the train being hauled north from its winter base at Carnforth, Lancashire, by a former British Rail Back Five loco called “Lancashire Fusilier”.
Tickets for the Jacobite start at £49 for adults and £28 for children. Because of Covid restrictions, the normal buffet car is being replaced by a refreshment trolley service but cream teas and champagne can be ordered in advance.