Nathan suffered a stroke on the morning of July 31, 2016 and was taken to Singapore General Hospital's Intensive Care Unit. He died in hospital on August 22, 2016 at 9:48 pm SST, aged 92. He was survived by his wife Urmila Nandey (known as Umi), their daughter Juthika and son Osith, three grandchildren, and his sister Sundari.