Clerk was in Derry during the siege in 1689 and received a bullet wound on his temple, leaving a sore over which he wore a black patch to the end of his days. It was not until after the siege that he began his studies for the ministry. He was ordained in 1697 by the Route presbytery as minister of Kilrea and Boveedy, County Londonderry. In 1721 he was the sole dissent to the synod's 'charitable declaration' enjoining forbearance towards the nonsubscribers to the Westminster Confession. The following year he and two others entered a strong protest against any compromise with the non-subscribing party. This party attacked him in his own presbytery, but though the matter was referred to the synod, the nonsubscribers were too much occupied in defending themselves to proceed with it.