John was traveling with his family and friends from London to the Utah Territory. They had departed Florence, Nebraska between August 6th and 10th as part of the Daniel D. McArthur company and were just two and a half weeks from their destination of Salt Lake City. As recounted by Marilyn Austin Smith in her biography of Ann Isacke (John’s wife), John had been in poor health for some time. He apparently contracted "mountain fever" - a "rickettsial bacteria [commonly] transmitted by wood ticks." His daughter Matilda noted that all day John had walked with lagging steps and pallid face. The company had stopped near the Three Crossings to camp for the evening. John insisted on putting up a tent for his girls, but in doing so fell down three times. In less than an hour, around midnight, he died.

Marilyn wrote, "the next morning before they left camp [John] was wrapped in canvas and laid to rest in a grave located near the campsite on the East Crossing of the Three Crossings of the Sweetwater River in Wyoming. A man by the name of Reed made a marker out of a broken box to mark his grave. Ann at the time was too ill to even raise her head. In great agony the grief stricken and ill family left John B. Farnes in a grave along the trail and continued on."