Born at Stadhampton, Oxfordshire, Owen was educated at Queen's College, Oxford, where he studied classics and theology and was ordained. Because of the "high-church" innovations introduced by Archbishop William Laud, he left the university to be a chaplain to the family of a noble lord. His first parish was at Fordham in Essex, to which he went while the nation was involved in civil war. Here he became convinced that the Congregational way was the scriptural form of church government. In his next charge, the parish of Coggeshall. in Essex, he acted both as the pastor of a gathered church and as the minister of the parish. This was possible because the parliament, at war with the king, had removed bishops. In practice, this meant that the parishes could go their own way in worship and organization.