Christ on The Cross, which was painted by Howson in 1964 when he was six, is to be sold at the McTear's Scottish Contemporary Art Auction on March 9, with half the proceeds going to Marie Curie Cancer Care.
The painting will be for auction with no reserve price.
The artist, known for his figurative imagery of muscular men as well as religious work, said: "I remember quite clearly painting it.
"I have always been religious - well a believer - and I was obsessed with the crucifixion.
"My grandmother was a great inspiration to me and she bought me a set of paints when I was four.
"Christ on the Cross with the world in the background was the first painting I completed."
He added: "My Uncle Bob was another very important figure in my life, a kindred spirit, and he gave me 10 shillings for the work. Unfortunately, he passed away a few years ago and the painting returned to me. I hope it raises a lot of money."
The painting was previously exhibited at a show called Peter Howson: A Retrospective which was held in the McLellan Galleries in Glasgow between July and September 1993.
Brian Clements, managing director at McTear's, said: "Christ on the Cross is an emotive piece. That it was created by a child is extraordinary."