Trump, who is now three weeks into his role as commander in chief, intended during the calls to make initial assessments of the men who have sometimes proved to be nettlesome partners to the US in its ongoing mission to rid their countries of militants.
However, Iraq's Prime Minister Haider al-Abadi used a portion of his half-hour conversation to insist Trump remove Iraq from a list of seven countries whose citizens he's tried to temporarily ban from entering the United States.
Trump told Abadi he would direct the US State Department toward finding a solution, according to an official description of the phone call from Baghdad, but didn't promise to remove Iraq from the list.
Along with Iraq, Trump's executive order barred citizens from Syria, Libya, Sudan, Iran, Yemen, and Somalia from entering the US for 90 days. The order is in legal limbo; a judge issued a temporary halt on the order and visa-holders from those nations have been able to board US-bound planes while the matter moves through courts.
Thursday night, the 9th Circuit Court of Appeals declined to reinstate Trump's travel ban.
In both Iraq and Afghanistan, US troops remain engaged in dangerous missions stemming from interventions under President George W. Bush more than a decade ago. Neither Trump nor his foreign counterparts expected to end the phone calls Thursday with new agreements on troop levels or strategy, according to people familiar with the conversations.
Indeed, Trump offered little clarity to Afghanistan's Ashraf Ghani about his long-term view on stabilizing the country's security situation.
"Afghanistan -- I would say that that's a tough situation, but we'll do something about it," Trump told reporters after his call on Thursday. "We'll be giving you some pretty good information soon."
In a formal readout of the conversation, the White House said Trump and Ghani "discussed opportunities to strengthen the bilateral relationship in areas such as security, counterterrorism cooperation, and economic development."
Earlier in the day, the commander of US troops in Afghanistan acknowledged before a congressional panel that the war, which began in 2001, was at an impasse.
"I believe we are in a stalemate," Gen. John Nicholson told the Senate Armed Services Committee. He said thousands of additional US troops were necessary for the NATO-led mission to train, advise and assist Afghan forces.
At the White House, press secretary Sean Spicer said Trump would follow the advice of his military advisers in determining troop levels in Afghanistan.
"I think the President will heed the advice of the generals and (Defense Secretary James) Mattis," Spicer said. "That conversation has yet to happen."
There are currently 8,400 US troops serving in Afghanistan as part of the NATO mission.
The phone calls were included in another round of telephone diplomacy for Trump, who has been dialing his counterparts at rapid pace since taking office last month. His conversations have come in spurts, including a marathon Saturday shortly after taking office that included contentious conversations with the leaders of France, Germany, Russia, Australia, and Saudi Arabia.
On Thursday, he also phoned the Emirs of two Gulf states, Tamim bin Hamad Al Thani of Qatar and Sabah al-Ahmad al-Jabir al-Sabah of Kuwait. Trump has pressed leaders of Sunni Arab nations to help establish safe zones inside Syria, which could provide refuge for civilians fleeing the country's bloody civil war.
It's a plan the previous administration rejected, arguing that enforcement of the safe zones would require additional US troops and questioning their effectiveness.