A total of 60 pledged delegates were at stake in the island primary contest.
Many Puerto Rico voters faced long lines and confusion over polling stations, many of which had closed since the Democratic primary in 2008. The island is also in the throes of an economic crisis after having accumulated more than $70 billion of outstanding debt.
Gov. Alejandro Padilla endorsed Clinton on Wednesday, calling her the best candidate to help the government out of the fiscal crisis.
Clinton also notched a victory in Saturday's caucuses in the U.S. Virgin Islands.
She is widely expected to secure the Democratic nomination on Tuesday, when Democratic voters in six states will head to the polls in the last multi-state primary day of the nomination race.