Early in 1881, Nutt had an attack of Bright's disease (nephritis). He was sick for more than two months. He died on 25 May 1881 at the Anthony House in New York City. Nutt's wife cried over his coffin at the funeral. She called him her "dear little boy", and said that he was "so good". Nutt was buried in Merrill Cemetery at Manchester, New Hampshire.