Al-Bashir later caught a return flight to Khartoum, the Sudanese capital.
He had risked arrest by leaving Sudan for his meeting with Mubarak, but Egypt, which has close ties with Khartoum, has called on the UN Security Council to suspend the ICC warrant.
Al-Bashir's visit to Cairo is his second foreign trip since the ICC indictment. He visited Eritrea on Monday.
Sudan's government said shortly after the ICC decision on March 4 that al-Bashir would defy the arrest warrant by travelling to an Arab summit in the Qatari capital, Doha, on March 27.
Sheikh Hamad bin Jassem Al Thani, the prime minister of Qatar, travelled to Sudan on Tuesday in an attempt to convince al-Bashir to attend the summit where they will focus on the situation in Darfur.
The Qatari prime minster said during his visit that Doha had been put under pressure by several parties to abstain from receiving al-Bashir.
"Doha would not acquiesce to such pressure while al-Bashir is absolutely free to take the appropriate decision about attending the Arab summit," the Qatari prime minister said.
But a series of Sudanese officials have released statements raising questions over the wisdom of the trip, prompting speculation they were preparing to send another representative instead.
Sudanese Islamic scholars have advised al-Bashir not to travel to the Arab League summit.
A trip to Qatar is viewed as more risky for al-Bashir than a visit to Egypt or Eritrea because it involves travelling through international airspace.
Qatar is not a member of the ICC and would have no legal obligation to arrest al-Bashir. Amr Mussa, the Arab League secretary-general, said last week that the 22-nation group would not act on the arrest warrant.
The Arab League and African Union, backed by China and Russia, have called on the UN Security Council to use its power to suspend the ICC indictment.
The United States, UK and France have said they see no point in halting al-Bashir's prosecution.
Aid worker killed
On Monday, a Sudanese relief worker was shot and killed in Darfur, a relief official said.
Adam Khater, manager of the Canadian-based Fellowship for African Relief, was shot dead in the western Darfur town of Kongo Haraza, Mark Simmons, the organisation's country director said.
"He was ambushed on Saturday by men who wanted his Thuraya satellite telephone," Simmons said.
"They came to his home on Monday evening to take the phone, but it wasn't there. The armed men then opened fire on him."
Aid workers have experienced increased hostility in Darfur after al-Bashir reacted to the ICC warrant, by expelling 13 international aid agencies from Darfur earlier this month.