While in London, Kirk, who still had a keen interest in fairy superstitions, met Bishop Edward Stillingfleet and his wife, Elizabeth. The bishop was a seventh son, and the couple, who were to have seven sons, asked what this might imply. In response Kirk wrote, and the curious Secret Commonwealth, addressed to Elizabeth Stillingfleet, Should you wish to be appraised of seventeenth century brawls in Killin, or second sight for widows, and much else, the Secret Commonwealth is for you.
Kirk married twice. His second wife was pregnant with their second child, Marjorie, when Kirk died, at Aberfoyle, on 14 May 1692. Interest in Kirk has persisted, partly because a successor at Aberfoyle, Patrick Graham (1750–1835), drew him to the attention of Sir Walter Scott who mentioned him in Rob Roy (1818). In his Sketches of Perthshire (1812), Graham related that Kirk did not die, but was ‘taken’ by the fairies whose secrets he had betrayed. According to Graham, Kirk reappeared at the baptism of his posthumous child. Manifesting himself to a ‘mutual relation’, the minister had asked that his brother-in-law, Thomas Graham of Duchray, cast a dagger above his head, to release him from fairyland, but, at the baptism, ‘in his astonishment’, Duchray failed to throw the weapon, leaving Kirk captive in fairyland.
Since then many distinguished folklorists have investigated the Fairy Minister, but this has meant that the importance of Kirk's work, as the scholar who was among the first to record highland folk-beliefs and to make the Bible accessible to highlanders, has sometimes been underestimated.
Louis Stott wrote the entry in the New Oxford Dictionary of Biography about Robert Kirk.