On the Restoration, Barlow was one of the commissioners for restoring the members of the university who had been ejected in 1648 and expelling the intruders. On behalf of John Owen, molested for preaching in his own house, he mediated with Edward Hyde, the Lord Chancellor. Henry Wilkinson was removed as Lady Margaret Professor of Divinity on 25 September 1660, in favour of Barlow. A few days before, on 1 September, he had taken his degree of D.D., one of a batch of loyalists created doctors by royal mandate. On the death of Barton Holiday in 1661, Barlow was appointed Archdeacon of Oxford, but there was a delay caused by a dispute between him and Thomas Lamplugh, ultimately decided in Barlow's favour, who was eventually installed on 13 June 1664. Barlow meanwhile was accused by Wood of underhand meddling in the election of Thomas Clayton to the wardenship of Merton College in 1661.