The Duke and Duchess Cambridge focused on education and the climate crisis during their official tour of the Asian country.
William and Kate left Pakistan at 4 p.m. local time (12.00 GMT) on Friday, an hour later than their scheduled departure, Efe news reported.
Before heading back to the UK, the royal couple visited an army canine center in Islamabad, where they walked two golden retrievers who are being trained to scout out hidden explosive materials.
They reached the capital on Friday morning after the plane carrying them had to abort its landing due to a storm.
On Thursday, they visited the Shaukat Khanum Memorial Cancer Hospital, founded in 1994 by Prime Minister Imran Khan.
William's mother, the late Princess Diana of Wales was a friend of Khan and visited the country in 1996 and 1997 to raise funds for the hospital.
William and Kate arrived in Pakistan on Monday and the next day visited a school to show support for girls' education before having lunch with Khan.
They also visited a center run by nonprofit SOS villages.
On Wednesday, they flew to the remote Chiatibo glacier, close to the Afghanistan border, to see the impact of climate change.
The royal couple enthralled the people of Pakistan, especially Kate who wore a number of outfits inspired by traditional Pakistani attire during the trip.
The Pakistan government said it hoped that the visit from the royal couple, the first since 2006, would help improve the country's image, which has been marred by terrorism and Islamic extremism.
"The Royal Couple's visit to Pakistan will improve the global image of Pakistan, increase the influx of foreign tourists," Pakistan Tehreek-e-Insaf tweeted.
Pakistan has witnessed high levels of sectarian and Islamist violence, which killed around 70,000 people between 2001 and 2015.
The situation has improved drastically in recent years, with a drop in extremist and terrorist activities after a series of military operations.
Despite this improvement, the visit has been marked by heavy security and the detailed itinerary of royals was not made public due to security concerns.
"This is the most complex tour undertaken by the Duke and Duchess to date, given the logistical and security considerations," Kensington Palace said in a statement.
( With inputs from IANS )