The Pentagon official who oversees military relations with Russia and Ukraine has resigned, a senior U.S. defense official confirmed to Fox News Tuesday.

The resignation of Evelyn Farkas, a Defense Department deputy assistant secretary, was reported first by Politico.

Farkas made the announcement Monday, the same day President Obama met privately for 90 minutes with Russian President Vladimir Putin in New York to discuss Russian intentions in the Middle East.

Russia has military deployments in worn-torn Syria and is backing rebel forces against neighboring Ukraine’s new, pro-Democratic government. Russia last year annexed the Ukrainian peninsula of Crimea.

A senior U.S. defense official said Farkas’ departure next month is not related to a policy dispute and that she is leaving the job after five years for an opportunity outside of government.

Still, her resignation comes at a crucial time for the Pentagon, which is now going to begin military contacts with Russia to try and stop the fighting in Syria.

Christine Wormuth, undersecretary of Defense for policy, purportedly is slated to lead the Pentagon in those engagements with the Russians.

Farkas’ resignation also comes just days after it was revealed that Gen. John Allen is stepping down this fall as point person for ISIS policy at the State Department.

Fox News Channel's Jennifer Griffin contributed to this report.