Causes Of Abdominal Pain At Nighttime. Pain in the abdomen at night can be due to following causes: 1  Indigestion of food: If you overeat or eat heavy food at night it may cause discomfort and pain in the abdomen after some time.2  It is one of the commonest causes of abdominal pain at night. This usually occurs 3 to 4 hours after you eat your dinner. 2  Kidney stone can cause abdominal pain at night. 3  However, kidney stone can also cause pain during day time. 4  Food poisoning: It is caused when you eat food contaminated with bacteria and viruses.