Mulki submitted the resignation during the meeting with Jordanian King Abdullah II, Al Jazeera reported, citing several sources.
According to the Doha-based broadcaster, the decision was made in order to ease tensions caused by the country's economic policies.
READ MORE: PHOTO and VIDEO of Jordan Rocked by Protests Against Austerity Measures
Following the resignation, the king asked Omar al-Razzaz, education minister in the outgoing government, to form a new government.
Massive protests have been engulfing the Jordanian capital and other cities since May 30, after the government proposed a set of economic reforms aimed at raising taxes and reducing spending in accordance with the International Monetary Fund's (IMF) requirements.
The legislative proposal is yet to be approved by the country's parliament. Jordan's prime minister and trade union representatives tried to negotiate a compromise on taxes on May 2, but the efforts ultimately failed and the protests continued.