Rambutan is a popular fruit widely cultivated in South East Asia. Rambutan seed is a by-product in canned fruit industry. The seed is rich in oil content. Rambutan seed oil contained high level of unsaturated fatty acids which are highly susceptible to microbiological, chemical and biochemical deteriorations. Oil microencapsulation is a popular method to prevent the change of oil quality during preservation. In this study, different protein preparations were alternatively used in microencapsulation of rambutan seed oil by spray-drying. Sodium caseinate, gelatin and soy protein isolate resulted in similar microencapsulation efficiency (67.3-69.9%) while the highest microencapsulation efficiency (73.6%) was obtained for whey protein isolate. The microencapsulation yield of sodium caseinate and gelatin was very low (25.6-28.5%) due to their high viscosity emulsions. Increased microencapsulation yield was observed for soy protein isolate (59.3%) while whey protein isolate showed the best microencapsulation yield (72.5%). Whey protein isolate also demonstrated the highest protective ability against oil oxidation during the accelerated storage of the spray-dried powder. Decrease in the ratio of rambutan seed oil/whey protein isolate from 1/1 to 1/4 enhanced the microencapsulation efficiency by 18% but did not change the microencapsulation yield.