Introduction: Since the WHO Classification of Tumours of the Digestive System has been published in 2010, resected pancreatic neuroendocrine tumours (pNETs) are graded as grade 1 (G1), grade 2 (G2) or grade 3 (G3) using the Ki67 labelling index (Ki67-LI). Endoscopic ultrasound-guided fine needle aspiration (EUS-FNA) is often used for diagnosis, but few studies have assessed its value for grading. Aims: The aims of this study were to compare the Ki67-LI obtained by cytological grading (cG) with that obtained by histological grading (hG) and to assess (1) the influence of tumour size and the number of counted cells on FNA grading as well as (2) the overall survival (OS) and progression-free survival based on cG. Materials and Methods: EUS-FNA was performed for 102 pNETs (57 resected). cG (200 cells counted) was done on all FNAs. For 29 FNAs, >2,000 cells were counted (14 resected). A comparison was made between hG and cG for the 57 resected patients. Patients were followed up until June 2016. Results: cG was consistent with hG in 39 of 57 patients with a concordance rate of 72% using a Ki67-LI cut-off of 5% for G1/G2. For Ki67-LI absolute values, the correlation was r = 0.443 and increased to r = 0.824 (p < 0.001) when only FNAs with >2,000 cells were counted. Twenty-one of 22 pNETs <2 cm had the same grading on cG and hG, whereas grading was discordant for 15 of 16 pNETs >2 cm. Thirty-eight patients died after 70.5 months of follow-up. OS for the whole cohort was 235 months and differed between cG1 (235 months), cG2 (36.3 months) and cG3 (10.9 months). Conclusion: cG of pNETs is more accurate when tumours measure <2 cm and more cells are counted on FNA. Discrepancies are seen between G2 tumours which are often considered G1 on FNA due to tumour heterogeneity. EUS-FNA is valuable to distinguish between patients with good (cG1) and poor (cG3) prognosis.