It will be Kerry's first visit to the department since taking on the top job at State earlier this year, DOD press secretary George Little told reporters Monday.
While declining to comment on the specific agenda for the meeting, "I am certain [Syria] will come up," he said.
Monday's powwow comes as the Pentagon and White House continue to grapple with possible options for American military intervention in the ongoing Syrian civil war.
Syrian rebels have battled government forces loyal to President Bashar Assad to a bloody stalemate in the country for the past two years.
Recent reports of chemical weapon use by Assad's forces against rebel positions inside Syria have increasingly set the stage for potential U.S. action.
On Monday, the U.N. panel investigating claims of human rights abuses in Syria walked back reports claiming rebel forces were responsible for chemical weapon use in the country.
Little declined to comment specifically on the panel's initial report and subsequent retraction of chemical weapon use in Syria.
"We are looking at all aspects" of possible chemical weapon use, by Assad or rebel forces in the country.
American officials are more than willing to "fold into the picture [any] information" U.N. investigators may have on the issue into DOD and intelligence assessments on Syria.
But he did note U.S. military and intelligence officials remain confident the Assad regime was "very likely" responsible for any chemical weapon use inside Syria.
While "no decisions have been made" regarding possible U.S. action in the country, the Pentagon remains "fully prepared for a range of contingencies" should the civil war boil over into a regional conflict.
Multiple airstrikes by Israeli warplanes inside Syria, targeting supposed armed shipments from Iran to Hezbollah fighters, have only ratcheted up tensions in the region.
President Obama defended Jerusalem's actions inside the country on Sunday.
"I continue to believe ... the Israelis justifiably ... have to guard against the transfer of advanced weaponry to terrorist organizations like Hezbollah," Obama said in a TV interview with Telemundo.
Iran has long been one of the Assad regime's top allies in the region, with Syria being a main thoroughfare for Iranian weapons shipments to Hezbollah and other Iranian-backed terror groups.
Administration officials have "always been concerned about the spillover effect" of the Syrian conflict, Little said Monday.
"This is a combustible region and [DOD] is aware of that," he said, declining to comment on whether Jerusalem notified the Pentagon prior to the airstrikes inside Syria.
Defense Department leaders are moving forward with "planning initiatives" in Jordan, Turkey and Israel in an attempt to contain the situation in Syria.
"We have been clear-eyed ... about the risks of outside intervention" in Syria, Little said, adding the ongoing conflict is "one of the most complex crises of the last generation."