In September, a Saudi court upheld a sentence of 10 years in prison and 1,000 lashes for Badawi, and he is expected to have 20 weekly whipping sessions until his punishment is complete.
The US, Amnesty International and Reporters Without Borders have denounced the flogging as a horrific form of punishment, and said Badawi was exercising his right to freedom of expression.
Witnesses said that Badawi, 30, was flogged after the weekly Friday prayers near Al-Jafali mosque as a crowd of worshippers looked on.
The blogger was made to stand with his back to onlookers as another man began flogging him, witnesses said, adding that Badawi did not make any sound or cry in pain.
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The faithful who had emerged from noon prayers watched in silence and were ordered by security forces not to take any pictures on their mobile phones.
On the eve of the flogging, the US slammed it as an "inhumane punishment".
Media watchdog Reporters Without Borders said the punishment was "barbaric" and noted its timing after Saudi Arabia condemned Wednesday's deadly attack on French magazine Charlie Hebdo.
Badawi, who has been in jail since 2012, is a "prisoner of conscience", said London-based Amnesty International, demanding his release.
Badawi is the co-founder of the Saudi Liberal Network along with women's rights campaigner Suad al-Shammari, who was arrested last October and also accused of "insulting Islam".