"Hagel and his Egyptian counterpart Sedki Sobhi discussed regional security in the Middle East, North Africa and the US-led coalition to counter Islamic State (IS)," Pentagon press secretary John Kirby said in a statement Saturday.
During the conversation, Hagel also thanked Sobhi for Egypt's role in brokering a ceasefire to end the Gaza crisis, Xinhua reported citing the statement.
"The two leaders reaffirmed their commitment to a strong bilateral relationship and agreed to continue to engage regularly," it said.
Sobhi, former army chief of staff, replaced Abdel-Fattah al-Sisi in March, after al-Sisi announced his resignation from the army in order to run for the presidential polls.
Al-Sisi won the presidential election held in May.
Al-Sisi led the ouster of Egypt's first freely-elected president Mohammed Morsi from the Muslim Brotherhood in July 2013, straining Egypt's ties with the US, a major aid donor.
The US temporarily halted its military aid to Egypt, including the delivery of 10 Apache helicopters, until April when President Barack Obama's administration decided to partially relax the suspension of aid.