Summary Candida auris is an emerging multidrug‐resistant yeast associated with invasive infection in healthcare settings. Recently, C auris cases in the United States have been detected in 11 states with the majority of cases in New York, New Jersey and Illinois. Rapid and accurate identification of C auris is critical for patient care and the implementation of public health measures to control the spread of infection. Our aim was to develop and validate a rapid DNA extraction method using the Roche MagNA Pure 96 instrument and a TaqMan real‐time PCR assay for reliable, high‐throughput identification of C auris. We evaluated 247 patient dermal swab samples previously analysed by culture/MALDI‐TOF. The diagnostic sensitivity and specificity were 93.6% and 97.2%, respectively. The assay was highly reproducible with a detection limit of 1 C auris CFU/10 μL. A receiver operating characteristic curve analysis of the real‐time PCR data showed an area of 0.982 under the curve, with a CT cut‐off value of ≤37.0. The turnaround time from DNA extraction to real‐time PCR results was approximately 200 samples/day. In conclusion, we successfully validated a rapid and high‐throughput method for accurate and reproducible identification of C auris with a significantly reduced turnaround time compared to culture/MALDI‐TOF based methods.