Any thing eaten on an empty stomach will have a better effect on your system. Papaya can be eaten in the morning or during lunch time. There's certainly no harm in eating at night also. Fruits are best eaten on empty stomach as their absorption by thee body's system is far greater as they get digested very easily.When your tummy is empty, the digestive juices concentrate on digesting only what comes inside and its been found that fruits take a shorter time to get digested compared to other foods. The papaya you eat will get digested in minutes and the vitamins and nutrients get absorbed quickly into your system.