Albert Protopopov, director of the department, told CNN that while frozen wolf cubs had been unearthed in the past, the discovery of an adult wolf's head was novel.
This is the first time the head of an ancient wolf has been found whose soft tissue has been preserved after 40,000 years, a grown wolf, he said.
Scientists are now building a digital model of the brain and the skull's interior for further study, Protopopov said. A team in Stockholm is analyzing the wolf's DNA.
An ancient cave lion cub, an extinct species preserved in Yakutia's vast areas of permafrost, is also being investigated.
As the planet warms, the region is likely to yield more remains, according to Protopopov.
The number of discoveries is growing because of the thaw of the permafrost, he said.
Earlier this year, scientists announced the discovery of liquid blood and urine within the frozen remains of a 42,000-year-old foal, also preserved in permafrost.
It was found by mammoth tusk hunters in Siberia's Verkhoyansk region. Scientists hope to clone the unusually well-preserved foal.In 2016, Russian scientists said an outbreak of anthrax in western Siberia was due to the thawing of a frozen carcass of an infected reindeer that died 75 years ago.