On January 6, 1925, Haynes, the Apperson brothers, and other automotive pioneers were awarded gold medals by the National Automobile Chamber of Commerce at a New York City auto exhibition for their contributions to the industry. On his return trip home, he contracted influenza and his health began to deteriorate rapidly. In March, he asked his son to take over his business interests while he traveled to Florida to seek rest in the warmer climate. His condition steadily worsened, causing him to cancel his planned trip to Cuba and return to Kokomo. He remained in his home, attended by his personal physician and a nurse until his death from congestive heart failure on April 13, 1925. Haynes' funeral was held in Kokomo before his interment at the city's Memorial Park cemetery.