Maybe. Since Puerto Rico is a Commonwealth and not a state, income derived from Puerto Rico and taxed by Puerto Rico is considered as Foreign Income. But, a U.S. citizen who spent at least two years in Puerto Rico before returning to the states (or a bona fide Puerto Rico resident who comes to the United States), may exclude the income derived from Puerto Rico on the U.S. return. In this case, any amount of Pension Income for with Pension Tax was paid to Puerto Rico before coming to the United States will not be taxed a second time.
However, if you were not outside long enough for the exclusion (or Puerto Rico is withholding tax even though you are now here in the states), the pension will be taxed in the United States. However, you can claim Foreign Tax Credit for any amount of tax you must pay to Puerto Rico on the pension. This credit is reported on Form 1116. Please see this FAQ with more information on how to do this in TurboTax: https://ttlc.intuit.com/replies/3302405
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