The historic ship was moved from its home along the Embarcadero by tug boat to a dry dock at BAE Systems in National City.
The repairs are expected to take about three weeks, but the exact timing won't be known until the ship is out of the water.
"We hope we don't find any surprises down there,'' said Robyn Gallant, the museum's director of public events.
A special ceramic coating will be applied to the Star of India's hull to help protect and preserve i,t and workers will put a fresh coat of paint on the ship, according to Gallant.
The Star of India is hauled out of the water every 10 years to undergo repairs to keep the ship in seaworthy condition and to meet U.S. Coast Guard requirements. Museum officials said they expect the repairs to cost $225,000.
"Because of this, the Star will not be able to go on her annual sail this November as we cannot incur all these costs in one fiscal year,'' according to a Maritime Museum statement.
The iron hull of the Star of India, billed as the world's oldest active ship, was laid in 1863 at a shipyard in the Isle of Man. The ship was first named the Euterpe but renamed the Star of India in 1906 when it hauled canned salmon from Alaska.
The Star of India was laid up in San Diego in 1923 and not fully restored until 1976.