The German president's wife, Bettina Wulff, presented Harry the Golden Heart statuette on Saturday at the country's largest TV charity gala, A Heart for Children.
The 26-year-old is patron of several children's and humanitarian aid charities. He also co-founded an organisation - Sentebale - to help young people in the African country of Lesotho.
Harry felt "hugely humble" to win the award and said it would encourage Sentebale and others in Lesotho "to redouble our efforts."
He told guests and the televised audience of millions "from the bottom of my heart Vielen Dank (thank you very much).
"But compared to so many people who devote their whole lives to restoring hope to children around the world, I have done very little."
Harry was following in the footsteps of past recipients of the award - actresses Salma Hayek, the 2009 winner, and in recent years Jane Fonda and Sharon Stone.
The prince arrived in a snowy Berlin which has been hit by the freezing conditions that have crippled transport in Europe. Among the guests were singers Kylie Minogue and Paul Anka.
A Heart for Children was started in 1978 by Axel Springer, the founder of the national German newspaper Bild.
