The central city is still struggling to deal with the impact of Typhoon Haiyan, which struck on November 8, causing more than 6,200 deaths and leaving tens of thousands of survivors still homeless.
Beckham was welcomed by hundreds who have been living in United Nations-provided tents outside a sports stadium.
Zafrin Chowdhury, a spokeswoman for the Unicef office in Manila, said Beckham was touched by the typhoon's impact and wanted to meet displaced children and their families.
Beckham exchanged high-fives and posed for pictures with children in a large white tent used as a classroom. Some showed him their art works.
He removed his shoes on entering a tent where a family has been living, stroking a sleeping infant's hands as he spoke with family members. Officials and Unicef staff did not say what he and the family members talked about during his 30-minute stay.
It is Beckham's second trip to the Philippines as a Unicef goodwill ambassador. He toured a shelter for former street children in Manila during his first visit in 2011 and also played an exhibition game with the Philippine national football team.
"He felt very touched by what happened and that he wanted to come back, not do anything else - no meeting, no media - just to focus on children and meet them, encourage them and see for himself the situation," Mr Chowdhury said.
Beckham is scheduled to visit a warehouse of the World Food Programme in nearby Palo, which was also heavily devastated.
The retired football icon and his wife Victoria donated some of their designer clothes and shoes to raise funds for the typhoon victims.
The storm displaced more than four million in more than 40 provinces in the central Philippines. At least 1,700 are still missing.
Beckham's visit followed separate trips to Tacloban in December by teen heart-throb Justin Bieber, US secretary of state John Kerry, Japanese defence minister Itsunori Onodera and Australian foreign minister Julia Bishop.