Relations between the churches have been strained for years, especially over Anglican ordination of women as priests, and the meeting at the Vatican was billed as an opportunity to reduce tensions.
Welcoming Archbishop of Canterbury Justin Welby, Francis called for Christians to work together to protect the "foundations of society" such as respect for human life and the institution of the family built on marriage.
Mr Welby said he hoped the proximity of their inaugurations would "serve the reconciliation of the world and the Church", while noting the difficulties ahead.
"The journey is testing and we cannot be unaware that differences exist about how we bring the Christian faith to bear on the challenges thrown up by modern society," he said.
Both men stressed the need for Christians to help poor people, and promote social justice and peace.
After addressing the pope and Vatican officials, Mr Welby went on to pray at the tomb of Saint Peter under St Peter's Basilica.