He returned to Oxford when the fighting was over, and survived the threat of ejection by the Parliamentary Visitors in control of the university with the help of Edmund Ludlow, a prominent Parliamentarian and his nephew by marriage.
When the parliamentarians occupied Oxford in 1646 he resisted the visitation, but was finally and physically ejected from All Souls in early 1648.
In 1648, the parliamentary visitors who were replacing the ejected Royalists at Oxford University made Sankey a Fellow of All Souls, Oxford and sub-warden.
In 1648 he was ejected from his fellowship by the parliamentary visitors, but during the Commonwealth practised physic with some success at Oxford.
A protest against the election was made by Charles Wheare, son of the previous professor Degory Wheare, who had been given the place by the parliamentary visitors.
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