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Background: Next-generation sequencing (NGS) is the most commonly used method for determining <i>BRAF</i> mutational status in patients with advanced melanoma. Automated PCR-based methods, such as the Idylla^TM system, are increasingly used for mutation diagnostics, but it is unclear what impact the choice of diagnostic method has on the management of melanoma. Objectives: To compare the concordance rate of <i>BRAF</i> V600 mutational analysis using Idylla^TM and NGS and to analyze the technical and clinical turnaround time. The clinical relevance is compared by analyzing the impact on the treatment decision. Methods: In this monocentric prospective cohort study, the <i>BRAF</i> mutation status of 51 patients was determined using both methods in parallel. Results: <i>BRAF</i> V600 mutation was detected in 23/51 cases (45%). Idylla^TM showed a 100% concordant result with a faster turnaround time (0.2 days) compared to NGS (12.2 days). In general, less tumor material was required for Idylla^TM than for NGS. Most patients received immunotherapy as a first-line therapy regardless of the <i>BRAF</i> V600 status. Conclusions: Idylla^TM testing proved to be a reliable and rapid alternative to NGS in the determination of <i>BRAF</i> V600 mutation. Although <i>BRAF.</i> status was available earlier, this had no influence on the treatment decision in most cases.