Background Either enucleation or more extended resection is performed to treat patients with pancreatic neuroendocrine tumor (pNET). Aim was to analyze the postoperative complications for each operation separately. Furthermore, independent risk factors for complications and incidence of pancreatic insufficiency were analyzed. Methods Retrospective all resected patients from two academic hospitals in The Netherlands between 1992 and 2013 were included. Postoperative complications were scored by both ISGPS and Clavien-Dindo criteria. Based on tumor location, operations were compared. Independent risk factors for overall complications were identified. During long-term follow-up, pancreatic insufficiency and recurrent disease were analyzed. Results Tumor enucleation was performed in 60/205 patients (29 %), pancreatoduodenectomy in 65/205 (31 %), distal pancreatectomy in 72/205 (35 %) and central pancreatectomy in 8/205 (4 %) patients. Overall complications after tumor enucleation of the pancreatic head and pancreatoduodenectomy were comparable, 24/35 (69 %) versus 52/65 (80 %). The same was found after tumor enucleation and resection of the pancreatic tail (36 vs. 58 %). Number of re-interventions and readmissions were comparable between all operations. After pancreatoduodenectomy, 33/65 patients had lymph node metastasis and in patients with tumor size <= 2 cm, 55 % had lymph node metastasis. Tumor in the head and BMI >= 25 kg/m(2) were independent risk factors for complications after enucleation. During follow-up, incidence of exocrine and endocrine insufficiency was significant higher after pancreatoduodenectomy (resp. 55 and 19 %) compared to the tumor enucleation and distal pancreatectomy(resp. 5 and 7 % vs. 8 and 13 %). After tumor enucleation 19 % developed recurrent disease. Conclusion Since the complication rate, need for re-interventions and readmissions were comparable for all resections, tumor enucleation may be regarded as high risk. Appropriate operation should be based on tumor size, location, and functional status of the pNET.