Background and Objective: The aim of this study was to investigate the diagnostic accuracy of ultrasound guided fine needle aspiration cytology (FNAC) and core needle biopsy (CNB) in different clinical scenarios for melanoma patients with lesions suspected of metastasis. Methods: We included all patients at our department attending follow-up after surgery for cutaneous melanoma, who had undergone either FNAC or CNB between December 2016 and June 2019. Biopsy results were classified into one of four categories and verified with follow-up including imaging, re-biopsy or histology upon excision. The diagnostic accuracy of FNAC and CNB were calculated overall, and based on location of suspected metastasis, reason for suspicion and stage. Results: We identified 232 biopsies in 164 patients; 109 FNACs and 123 CNBs. For FNAC, overall sensitivity was 83.3% and negative predictive value was 88.4%. For CNB, overall sensitivity was 92.4% and negative predictive value was 88.0%. There were significantly fewer nondiagnostic results using CNB compared to FNAC (χ₁² = 6.7, p = 0.0095). Conclusions: There were no significant differences between the diagnostic accuracy of FNAC and CNB in the different clinical scenarios. We found significantly fewer nondiagnostic biopsies when using CNB, although this may reflect the type of lesions selected for each approach.