The move is seen as part of international sanctions on the country over its disputed nuclear program. The West has imposed banking and insurance sanctions on Iran since it suspects Iran is pursuing nuclear weapons, a charge Tehran denies.
At a Tehran shopping mall, owners of mobile phones and tablets said Thursday that they had received the message via email from the company late the night before. Retailers said they had no power over the decision.
"We have heard about it, but we are only responsible for hardware here, not software and apps," shopkeeper Bijan Ashtiani said.
In the message, Samsung said that it cannot provide access to the store, known as Samsung Apps, in Iran because of "legal barriers." It apologized to customers in emailed statement seen by the Associated Press on Thursday.
Samsung's offices in Tehran could not be immediately reached for comment due to the weekend there, and its headquarters in South Korea did not immediately respond to a request.
The decision quickly provoked ire on social media.
"Samsung is to stop its apps in Iran, oh how we appreciate our officials," wrote Bahareh, a Twitter user blaming Tehran's policy. Another, named Armin, pointed at the technology giant itself, saying: "Now, Samsung's sanctions honor us as well!"
Samsung spokesman Chris Jung in Seoul said the company is still looking into the matter and could not confirm any details.
Unlike Apple, Microsoft and Adobe, Samsung has provided localized services to Iranians in their native Persian language. In 2012, Finnish communications giant Nokia stopped its services in the country.