Background: Non-traumatic small bowel perforation, though uncommon, is a serious and life-threatening condition requiring prompt diagnosis and management. This study aimed to examine the etiological factors, clinical presentations, surgical outcomes, and patterns of morbidity and mortality associated with non-traumatic small bowel perforation in a tertiary care center in Northeast India. Methods: This prospective study, conducted at RIMS Hospital, Imphal, included 30 cases of non-traumatic small intestinal perforation. Cases involving trauma, anastomotic dehiscence, or lack of consent were excluded. Detailed histories, clinical examinations, radiological evaluations, and laboratory tests were performed. Emergency exploratory laparotomies confirmed perforations, and biopsy samples were collected for histopathological examination. Postoperative care involved antibiotics, analgesics, and fluid therapy, with complications managed appropriately. Data were analyzed using SPSS, with qualitative variables as frequencies/percentages and quantitative data as means/standard deviations or medians/ranges. Postoperative morbidity and mortality were carefully documented. Results: The mean age of the study population was 46.5 ± 5.2 years, with a male predominance (83.3%). Abdominal pain (100%) and distension (96.7%) were the most common presenting complaints. Duodenal ulcer perforations were the leading cause (60%), followed by typhoid (30%) and tuberculous perforations (10%). Surgical techniques included Graham’s omental patch (60%) and primary closure (40%). Postoperative complications included paralytic ileus (23.3%), wound sepsis (16.7%), and septicemia (10%). The median hospital stay was 10 days. Conclusion: Duodenal ulcers were the predominant cause of non-traumatic small bowel perforations in this study. Despite complications, early surgical intervention and postoperative care effectively managed morbidity and mortality.