Candida auris has emerged as a significant global nosocomial pathogen. This is primarily due to its antifungal resistance profile, but also its capacity to form adherent biofilm communities on a range of clinically important substrates. While we have a comprehensive understanding how other Candida species resist and respond to antifungal challenge within the sessile phenotype, our current understanding of C. auris biofilm mediated resistance is lacking. In this study we are the first to perform transcriptomic analysis of temporally developing C. auris biofilms, which were shown to exhibit phase and antifungal class dependent resistance profiles. A de novo transcriptome assembly was performed, where sequenced sample reads were assembled into a ~11.5 Mb transcriptome consisting of 5848 genes. Differential expression (DE) analysis demonstrated that 791 and 464 genes were up-regulated in biofilm formation and planktonic cells respectively, with a minimum 2-fold change. Adhesin related GPI-anchored cell wall genes were up-regulated at all time-points of biofilm formation. As the biofilm developed into intermediate and mature stages, a number of genes encoding efflux pumps were up-regulated, including ATP-binding cassette (ABC) and major facilitator superfamily (MFS) transporters. When we assessed efflux pump activity biochemically, biofilms efflux was greater than planktonic cells at 12 and 24 h. When these were inhibited, fluconazole sensitivity was enhanced 4 to 16-fold. This study demonstrates the importance of efflux mediated resistance within complex C. auris communities and may explain its resilience to a range of antimicrobial agents within the hospital environment.