Raif Badawi was flogged after Friday prayers outside a mosque, the witness said.
His feet and hands were bound but his face was visible. He remained silent during the lashings.
Badawi was sentenced last May to 10 years in prison and 1,000 lashes.
He had criticised Saudi Arabia’s powerful clerics on a liberal blog he founded.
Amnesty International said Badawi would receive 50 lashes once a week for 20 weeks.
Saudi Arabia’s close ally, the United States, called on authorities to cancel the punishment.