In 1659 he sought to be reconciled with George Fox, from whom he had become estranged, but was rebuffed. William Dewsbury was at last instrumental in bringing a reconciliation, and James Nayler resumed his Quaker service, 'living in great self-denial and very jealous of himself'.
In 1660, after his release, he set out on foot for the north, intending to go home to his wife and children. On the way, he was robbed and bound, and found towards evening in a field. He was taken to a Friend's house near King's Ripton, where he died. These were some of his last words:
There is a spirit which I feel that delights to do no evil, nor to revenge any wrong, but delights to endure all things, in hope to enjoy its own in the end. Its hope is to outlive all wrath and contention, and to weary out all exaltation and cruelty, or whatever is of a nature contrary to itself. It sees to the end of all temptations. As it bears no evil in itself, so it conceives none in thoughts to any other. If it be betrayed, it bears it, for its ground and spring is the mercies and forgiveness of God. Its crown is meekness, its life is everlasting love unfeigned; it takes its kingdom with entreaty and not with contention, and keeps it by lowliness of mind. In God alone it can rejoice, though none else regard it, or can own its life. It's conceived in sorrow, and brought forth without any to pity it, nor doth it murmur at grief and oppression. It never rejoiceth but through sufferings; for with the world's joy it is murdered. I found it alone, being forsaken. I have fellowship therein with them who lived in dens and desolate places in the earth, who through death obtained this resurrection and eternal holy life.