The Dynasty foundation's board made the decision on Monday, according to a statement on its website.
The foundation has provided support for scientists, fellowships and visits to Russia by foreign scientists.
Russian law requires non-governmental organizations that receive funding from abroad to register as "foreign agents," a term carrying Cold War spying connotations.
The Justice Ministry declared Dynasty a foreign agent because its Russian head funds it with money from foreign bank accounts.
Dynasty was to allocate about USD 8 million in grants this year. The foreign agent label would have made it nearly impossible for it to support state-funded libraries, schools and colleges.