Enlisted in the Eastern Association army; by 1644 he was a zealous Lieutenant in Oliver Cromwell's cavalry regiment. As a religious radical, Packer clashed with Major-General Lawrence Crawford, who had him arrested for disobedience. Cromwell intervened to have him released, leading to the bitter dispute between Cromwell and Crawford. On the formation of the New Model Army in 1645, Packer became a captain in Fairfax's regiment of Horse. He was with Fairfax at the siege of Colchester in 1648, then served as a Major in Cromwell's regiment on the Scottish campaign of 1650.