Towler, who is programme director for Save the Children in Wales, has worked with the charity on policy, advocacy and research. He is also chair of the United Nations Convention on the Rights of the Child Monitoring Group for Wales.
As commissioner he will be an independent advocate for children in Wales.
He said: "I'm really excited by the opportunity and look forward to working with children and young people across Wales."
The first children's commissioner for Wales, Peter Clarke, died from cancer in January.