Mr Khan said the UAE's financial support showed its continued commitment and steadfast friendship to Pakistan over the years.
Al Nahyan, who is also deputy chief of the UAE's armed forces, "will have a one-on-one meeting" with Khan, the statement said.
According to a joint statement issued after the UAE royal's visit, bilateral relations and regional and global issues were discussed during PM Khan and Sheikh Mohammed's meeting. the crown prince was also briefed by PM Khan on the Kashmir issue.
Sheikh Mohammed departed for the UAE Sunday afternoon.
The UAE government's financial assistance comes as Pakistan is negotiating a United States dollars 8 billion bailout package from the International Monetary Fund (IMF) to overcome a severe balance-of-payments crisis that threatens to cripple the country's economy.
Soon after assuming his role as prime minister of Pakistan after a landslide victory of his political party in July a year ago, Imran Khan gave priority to establishing a cordial relationship with both the UAE and Saudi Arabia.
This was the third interaction between the leadership of Pakistan and UAE in less than three months.
Mr Khan inherited a looming economic crisis when he took office five months ago, with the Pakistan's foreign reserves almost gone and a growing balance of payments crisis.
While the former cricketer's government is in negotiations with the International Monetary Fund, Mr Khan has repeatedly said he is reluctant to rely on the Washington-based body.
The fund has financed eight development projects in Pakistan with a total value of AED 1.5 billion, including AED 931 million in grants.
The report quoted a cabinet member as saying that the UAE package is exactly the same size and has the same terms and conditions as those given by Saudi Arabia. The last of three Saudi cash payments is expected later this month.
Special Assistant to the Prime Minister on Overseas Pakistanis Zulfi Bukhari said the UAE was Pakistan's largest trading partner in the Middle East and a major source of investments.
The rupee has been devalued twice since he took power, and while his ruling Pakistan Tehreek-e-Insaf (PTI) appears to remain the most popular party, disenchantment and rising costs may soon begin to eat into his popularity.
The prime minister congratulated the leadership of the UAE for declaring 2019 as the year of tolerance. The national anthems of both countries were played, and Sheikh Mohammed bin Zayed was given a fly-past by an impressive formation of JF-17 fighter jets. Hardliners paralysed the country with protests for three days until Mr Khan agreed to allow a petition to review her supreme court acquittal.
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