Petroleum supplies were not affected by the attack at 4.40am local time. The fire was controlled and did not result in any injuries or casualties, Saudi state news agency SPA reported.
“The refinery's operations and supplies of petroleum and its derivatives were not affected,” an Energy Ministry spokesman said.
The ministry did not indicate where the attack originated and no one has yet claimed responsibility.
Brent, the global benchmark for two thirds of the world's oil, was trading 0.36 per cent lower at $109.10 a barrel at 7.24am UAE time on Friday while West Texas Intermediate, the gauge that tracks US crude, was 0.19 per cent higher at $106.20 a barrel.
The attacks have been focused on oil installations, including the pipelines and storage units of Saudi Aramco, the world's biggest corporate oil producer.
“These repeated acts of sabotage and terrorism on vital installations and civilian structures … do not just target the kingdom but aim to undermine the security and stability of global energy supplies,” the Energy Ministry spokesman said.
Arab nations, including the UAE, Egypt and Jordan, as well as the Arab Parliament, condemned the attack.
The UAE's Ministry of Foreign Affairs said: "This attack is a cowardly terrorist act and a war crime that requires a response against threats to the security and safety of civilians and vital facilities".
Saudi Arabia has accused Iran of arming the Houthis and has blamed Tehran for past attacks. Tehran denies the accusations.
The Houthis took over Sanaa in 2014, prompting an intervention by the Saudi-led coalition the following year.