Samuel accompanied the Marquis of Ormonde to Ireland as private chaplain in 1632. He was installed a prebendary of the diocese of Ossory on 5 June 1634, appointed rector of Knockgraffon, Tipperary, and chancellor of Cashel in 1636. On 14 November 1638 he was created dean of Clonfert in Galway. On the outbreak of the Catholic rebellion in October 1641, Pullen, who was then living in Cashel, Tipperary, was plundered of all his goods, to the value of four or five thousand pounds, and, with his wife and children, only escaped murder by the protection of a Jesuit father named James Saul, who sheltered him for three months. On his escape to England, Pullen became chaplain to Aubrey de Vere, 20th Earl of Oxford. Invited by the Countess of Oxford to hear a sermon of a popular Puritan preacher, an alleged shoemaker, Pullen recognised in the preacher his former benefactor, the Jesuit, in disguise. Pullen contrived that Saul should quit Oxfordshire without exposure.