No one was injured in the incident, which occurred around 5 am when flames broke out in the rear engine of the vehicle on the A-2 Highway, Uri cantonal police said.
The bus was carrying 45 people, including 38 children, on their way to a ski camp in Italy, cantonal police said.
The fire occurred just before the bus was set to enter the 16.4-kilometre tunnel, police said.
The driver parked the vehicle on the shoulder of the highway and the passengers disembarked.
Gotthard fire protection workers put out the blaze, which caused damage estimated at 12,000 francs, police said.
The bus passengers were brought to an industrial yard where they awaited a replacement bus to take them on to their destination.
Police said they are investigating the cause of the fire.
The incident comes less than three weeks after a fatal crash, followed by a fire, closed the Gotthard tunnel for seven hours on December 20th.
The driver of a car died after it collided head on with a truck in the south end of the tunnel.
Safety measures in the tunnel linking the canton of Uri with Italy have been stepped up since 11 people lost their lives and a further 128 people were injured after two trucks collided there in a horrific accident 11 years ago.