By 1883, it was clear that Kennedy was far from well. The General Assembly that year granted his request for permission for Dingwall to call a ‘colleague and successor’, which would have allowed him to retire from the principal burden of his charge. Kennedy himself took an extended convalescent break on the Continent that year. Hoping to return to Dingwall the following spring, he commenced the journey home but reached only as far as Bridge of Allan, where, on 28 April 1884, John Kennedy died. He was buried in the grounds of the Free Church in Dingwall, as later were his widow and his unmarried daughter. To this day, the Kennedy monument stands alone on that ground, a unique mark of respect to the town's most renowned minister. So widespread was the mourning that a whole volume was published of the obituaries, sermons and posthumous tributes to Kennedy's ministry.

But the full extent of Kennedy's influence is seen only in a broader retrospect. By his preaching and pastoral guidance, he helped to guide the trajectory of evangelicalism in the Highlands in a thoroughly conservative direction that emphasised the authority of Scripture, Divine sovereignty and the need for personal self-examination, and that maintained sacramental practices reflecting these priorities. In his historical and biographical writings, Kennedy challenged readers of his own day to uphold the same priorities as the historic Highland Church, and built a new confidence and cohesion around its distinctive practices in opposition to trends in wider evangelicalism. In his leadership of the Highland part of the constitutionalist party, Kennedy was demonstrably significant in forging a resolute core unchangeably committed to the Free Church constitutional position of 1843. In controversy in the public sphere, Kennedy opposed movements for change in worship, evangelism and Biblical criticism, and helped to unite the Highland people of the Free Church in general opposition to the multifarious revolutions of the Victorian Church, which he saw as a single movement at heart.

For Kennedy, the evangelicalism of the Highlands was nothing less or more than the religion commanded in Scripture, enacted in the Reformation, codified in the Westminster Confession and conserved in the stand of the Disruption Free Church. The Highland Church was not pursuing an eccentric cultural tradition, but rather maintaining the Calvinistic heritage that the majority of the Lowland evangelicalism seemed increasingly content to abandon.