The visit comes just over two weeks after Tracy was given access to US journalist Evan Gershkovich, arrested in Russia in March on espionage charges.
The prison visit also comes after Washington said "there was a proposal on the table for (the release of) Paul" in March.
Washington says both Whelan and Gershkovich are "wrongfully detained" and has accused Moscow of "hostage taking."
The US embassy in Russia said Tracy travelled to the IK17 prison in Mordovia -- some 400 kilometres (250 miles) southeast of Moscow -- to visit Whelan in a region notorious for its harsh prisons.
"The US government will continue to engage Russian authorities on his case so Paul can come home as soon as possible," it said.
It called working on his release an "absolute priority."
National Security Council spokesman John Kirby said on CNN earlier Thursday that his government was "energetically trying" to get Whelan released.
"We will urge the Russians to accept that proposal so we can get him out of there," he said.
He said US officials are also "in initial conversations... trying to get the Russians to agree to release Evan."
He added the United States wanted "more consular access" to the journalist.
In March, US Secretary of State Antony Blinken said Washington had put forward a "serious proposal" that Moscow "should accept" for Whelan's release.
Whelan was arrested in 2018 and sentenced to prison two years later for alleged spying.
Russia and the United States accuse each other of political arrests and have led several rounds of high-profile prisoner exchanges in recent years.
Last year the United States secured the release from Russia of basketball star Brittney Griner, jailed on drugs charges and another former Marine, Trevor Reed, imprisoned for assaulting a Russian police officer.
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