By 1800 James Magee's health was failing. In the fall of 1800 Magee and his wife joined Thomas Handasyd Perkins on a trip to Ballston Spa and Saratoga Springs, New York, partly for Magee's health. A few months after returning to Boston James Magee suffered the last of several strokes. He died on 2 February 1801, in his home at Roxbury. On 5 February 1801 he was buried, probably in the Central Burying Ground in Boston Common, in the tomb he had purchased in 1790, in which his wife and four of his children were later interred.
