It was not immediately clear if Shanahan and Khalilzad would be conducting joint discussions during their trips.
The withdrawal of foreign forces from Afghanistan is one of the Taliban's key demands in peace negotiations with United States officials. Kabul is also concerned that a sharp drawdown of American forces could lead to chaos in the region.
Reports that US President Donald Trump wants to withdraw about half of the estimated 14,000 US forces in Afghanistan, have raised concern among Afghan and regional officials about what effect it might have on security in the country.
Shanahan, who is also due to meet General Scott Miller, the top United States and North Atlantic Treaty Organisation commander in Afghanistan, told reporters aboard his flight to Kabul that he had no instructions from Washington to begin a withdrawal.
He also met his Afghan counterpart Asadullah Khalid in Kabul and reassured him that the USA military would not abandon Afghan soldiers in their battle against the militants.
Zalmay Khalilzad, US special representative for Afghanistan reconciliation, recently announced that US and Taliban officials had reached an agreement in principle for a peace deal.
The acting defence chief also said he could not make any guarantees because USA peace envoy Zalmay Khalilzad was leading the talks.
Ghani proposes the Jirga at a time that Taliban has constantly refused to hold direct talks with the Afghan government.
Khalilzad, the former US ambassador to Kabul, had a six-day consultation with Afghan Taliban last month in Qatar.
Confusion has surrounded what appeared to be a decision in December to withdraw as many as half the 14,000 USA troops in Afghanistan, an indication of the contradictory messages that have often characterized Trump's foreign policy and internal debates about a war that even military leaders characterize as a stalemate.
Afghanistan and neighbouring countries are also concerned about the effect of a sudden withdrawal of USA forces on the region. "It's not about the USA, it's about Afghanistan", Shanahan said.
An Afghan official, speaking on the condition of anonymity, told Reuters that even the suggestion of US troops leaving was risky.
He has said since then there has been progress on the future of U.S. troops in Afghanistan.
The U.S. denies that any timeline for a withdrawal has been agreed yet with the Taliban, though CBS News senior national security correspondent David Martin reported just before Christmas that the Pentagon had been ordered to start planning the withdrawal of roughly 7,000 troops.
A spokesman of the Defense Ministry, Ghafoor Ahmad Jawed, said military operations by Afghan forces are ongoing in at least 15 provinces.