The sixth-in-line to the throne was on June 23 in Pitseng to open the new building at the Phelisanong Children’s Centre.
But his wife, the Duchess of Sussex, did not accompany him.
Kensington Palace confirmed Harry was not on a state visit but was carrying out a personal commitment on a “private visit”.
Heart-warming pictures posted on social media by Phelisanong Children’s Centre show a relaxed Duke meeting the centre’s staff members and being playful with the children.
During the visit, he unveiled a plaque at the new community hall, donated by his charity Sentebale to mark the official opening.
Despite the absence of Meghan, the Duke didn’t travel alone to Lesotho, but was joined by friend and Sentebale ambassador Adam Bidwell.
Following the footsteps of his mother, Princess Diana, Harry co-founded Sentebale with Prince Seeiso of Lesotho in 2006.
The charity, whose name mean ‘forget me not’, was created in a bid to improve prospects for the thousands of children and young people affected by HIV/Aids in the country.
Harry first visited Lesotho in 2004, where he developed a close bond with four-year-old Mutsu Potsane.
Prince Harry returned to Lesotho to open a community hall on behalf of his charity
Prince Harry co-founded Sentebale in 2006
In 2016 the prince was reunited for the first time with the boy, now 18, and earlier this year he was invited to attend Harry and Meghan’s Royal Wedding on May 19.
Prince Seeiso, who was also invited to the wedding at Windsor Castle, praised Harry for his work with Sentebale during an interview following the ceremony.
He said: “The young Harry who first arrived in Lesotho in 2004 is now a grown man getting married.
“I’ve come here with all the wishes of Lesotho, I’m not here on my own behalf I’m here representing the entire nation who are so happy.”
Prince Harry first visited the country in 2004
Prince Harry unveiled the community hall with his friend and Sentebale ambassador Adam Bidwell
Speaking about the charity that he and Harry had co-founded, the prince added: “We started this from zero.
“He has always had the passion, he has always had the vision.”
Prince Seeiso also said all the children who benefit from their charity “love” Prince Harry.
Prince Harry was last seen with his wife Meghan at Royal Ascot on June 20, where the couple was pictured holding hands and chatting peacefully during the races.