Construction workers had been drilling into the ground when the bomb exploded, a spokesman for the fire department said in a statement.
The blast was heard several kilometres away and scattered debris hundreds of metres, according to local media reports.
Images showed a plume of smoke rising directly next to the train tracks.
Bavaria interior minister Joachim Herrmann told Bild that the whole area was being searched.
Although trains started up again from 3pm, the rail operator said there would still be delays and cancellations to long-distance and local travel in the Munich area until evening.
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According to the fire service, the explosion happened near a bridge that must be passed by all trains travelling to or from the station.
The exact cause of the explosion is unclear, police said. So far, there are no indications of a criminal act.
WWII bombs are common in Germany
Some 75 years after the war, Germany remains littered with unexploded ordnance, often uncovered during construction work.
However, most bombs are defused by experts before they explode.
Last year, seven World War II bombs were found on the future location of Tesla’s first European factory, just outside Berlin.
Sizeable bombs were also defused in Cologne and Dortmund last year.
In 2017, the discovery of a 1.4-tonne bomb in Frankfurt prompted the evacuation of 65,000 people — the largest such operation since the end of the war in Europe in 1945.