The vessel carrying 56 people was intercepted by Malaysian maritime authorities near the northwestern island of Langkawi, said navy chief Ahmad Kamarulzaman Ahmad Badaruddin.
Its arrival came as fears grow about conditions in overcrowded camps for the minority fleeing violence in Myanmar. Nearly 700,000 Rohingya have sought shelter in southern Bangladesh since Myanmar launched a brutal crackdown last August.
"All 56 passengers, mostly children and women, are safe but tired and hungry," said the navy chief.
"The boat and its passengers will be handed over... to the immigration authorities."
Rohingya migrants trying to travel south by boat have been rare since Thai authorities clamped down on regional trafficking networks in 2015, leaving thousands of migrants abandoned in open waters or jungle camps.
Rohingya refugees fleeing to Bangladesh have arrived to find cramped settlements and often squalid conditions in the Cox's Bazar district. Hundreds of thousands of Rohingya who fled previous waves of persecution are already living in the district.
Many of the Rohingya ensnared in the 2015 boat crisis ended up in Muslim-majority Malaysia and Indonesia because Thailand stuck to a policy of not accepting the vessels.
There are nearly 70,000 Rohingya refugees and asylum-seekers living in Malaysia, according to the most recent statistics from the UN refugee agency.
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