The corporal punishment was carried out after Friday prayers outside the Al-Juffali mosque in Jeddah. It is the site where executions are carried out, earning it the grisly nickname "Chop Chop Square".
Amnesty International, which has been campaigning for Badawi, also confirmed he was flogged.
Speaking to IBTimes UK, an Amnesty spokesperson said: "We believe he will be taken back to prison. As far as we understand, he will be lashed 50 times every week until the punishment is completed."
Badawi, who co-founded the Saudi Arabian Liberals website, was arrested in 2012 for promoting public debate on his site, which has been closed since.
He was sentenced to 10 years in prison and 1,000 lashes in May last year because of accusations that he had insulted Islam.
He was also charged with apostasy, which carries the death penalty in the Saudi Kingdom, but he was cleared of this crime in 2013.
The Jeddah Criminal Court also ordered him to pay one million Saudi riyals (£157,220).
The news of Badawi's punishment sparked outrage worldwide with dozens of activists and NGOs condemning Saudi Arabia for its crackdown on freedom of speech.
Many have taken to social media to urge the Kingdom to halt the punishment.