BIRC3 is a recurrently mutated gene in chronic lymphocytic leukemia (CLL) but the functional implications of BIRC3 mutations are largely unexplored. Also, little is known about the prognostic impact of BIRC3 mutations in CLL cohorts homogeneously treated with first line fludarabine, cyclophosphamide, and rituximab (FCR). Immunoblotting analysis showed that the non-canonical NF-kB pathway is active in BIRC3 mutated cell lines and primary CLL samples, as documented by the stabilization of MAP3K14 and by the nuclear localization of p52. In addition, BIRC3 mutated primary CLL cells are less sensitive to fludarabine. In order to confirm in patients that BIRC3 mutations confer resistance to fludarabine-based chemoimmunotherapy, a retrospective multicenter cohort of 287 untreated CLL receiving first-line FCR was analyzed by targeted next generation sequencing (NGS) of 24 recurrently mutated genes in CLL. By univariate analysis adjusted for multiple comparisons BIRC3 mutations identify a very poor prognostic subgroup of patients failing FCR [(median progression free survival (PFS): 2.2 years, p < 0.001] similar to cases harboring TP53 mutations (median PFS: 2.6 years, p < 0.0001]. BIRC3 mutations maintained an independent association with an increased risk of progression with a hazard ratio (HR) of 2.8 (95% C.I. 1.4-5.6, p = 0.004) in multivariate analysis adjusted for TP53 mutation, 17p deletion and IGHV mutation status. If validated, BIRC3 mutations may be used as a new molecular predictor to select high-risk patients for novel frontline therapeutic approaches.