At the time the race was called, she had 64 per cent of the vote to 34 per cent of the vote for rival Vermont Senator Bernie Sanders.
Now, Clinton needs 30 more delegates of the 2,383 needed to secure the nomination, Politico reported.
Clinton is closing in on a historic nomination as the first female presidential nominee with one more round of states — California, New Jersey, New Mexico, South Dakota and Montana — set to vote on Tuesday.
Her nomination would become official during July’s Democratic National Convention in Philadelphia.
So far, Clinton has clinched a total of 2,354 votes (superdelegates: 547, pledged: 1,807) and Sanders has garnered 1,561 (superdelegates: 46, pledged:1,515).
Neither candidate campaigned extensively in Puerto Rico, instead they are focusing more on resources and campaign events in California with its 546 delegates.
Clinton, who won the territory by a landslide margin in 2008 over then senator Barack Obama, was the heavy favourite to win the territory’s primary.
In her two terms as senator from New York – the state with the largest population of Puerto Rican Americans – she gained a strong degree of familiarity with the island. Those relationships helped her build strong institutional support from top Puerto Rico Democrats, including Governor Alejandro Padilla.
Clinton’s Puerto Rico victory follows her win in the US Virgin Islands caucuses on Saturday.