Trump "expressed concern over the vast wildfires afflicting Siberia. The leaders also discussed trade between the two countries," according to a brief statement from Trump's press office.
Earlier, the Russian state-run news agency Ria reported that Washington initiated the call to the Kremlin, and that Trump offered US help with the fires.
Around three million hectares (7.4 million acres) of land in the center and east of Russia were burning as of Wednesday, authorities said.
The smoke has affected not only small settlements but also major cities in Western Siberia and the Altai region, as well as cities in the Urals such as Chelyabinsk and Yekaterinburg. Air travel has also been disrupted.
According to the Ria report, Putin praised the offer of help as a good sign for improvement in US-Russian relations.
Ties between Washington and Moscow have been strained by differences over Syria and Ukraine.
Relations are also complicated by controversy swirling around Trump's former business interests in Russia, and US intelligence agencies' conclusion that the Kremlin meddled in the 2016 election.