The Mexican foreign ministry said it would send about 30 tonnes of bottled water, insect repellant and other supplies to help the US territory, where the monster storm made landfall on September 20, leaving more than 30 people dead and thousands homeless.
Mexico will also send a team of specialists to help restore electricity to some 93 percent of the island left without power by the hurricane, it said.
US-Mexican relations have been strained since Trump came to power in January after a campaign laced with anti-Mexican rhetoric, including a promise to make Mexico pay for a wall on the border.
Mexico's aid shipment comes as the country recovers from its own disasters -- earthquakes on September 7 and 19 that caused an estimated $2 billion in damages.
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Mexico also offered aid to the United States after Hurricane Harvey ravaged Texas last month. But US authorities were slow to accept, and after the September 7 earthquake Mexico revoked the offer, saying it had to concentrate on the relief effort at home.
The United States sent rescue brigades to Mexico after the second earthquake and announced it would donate $100,000 in aid.
Trump, who visited Puerto Rico on Tuesday, is expected to ask Congress for a $29 billion emergency relief package for the island.