Cyclin dependent kinase 4/6 (CDK4/6) inhibitors (CDK4/6i) are effective in breast cancer; however, drug resistance is frequently encountered and poorly understood. We conducted a genomic analysis of 348 estrogen receptor-positive (ER+) breast cancers treated with CDK4/6i and identified loss-of-function mutations affecting FAT1 and RB1 linked to drug resistance. FAT1 loss led to marked elevations in CDK6, the suppression of which restored sensitivity to CDK4/6i. The induction of CDK6 was mediated by the Hippo pathway with accumulation of YAP and TAZ transcription factors on the CDK6 promoter. Genomic alterations in other Hippo pathway components were also found to promote CDK4/6i resistance. These findings uncover a tumor suppressor function of Hippo signaling in ER+ breast cancer and establish FAT1 loss as a mechanism of resistance to CDK4/6i. Display omitted •FAT1 or RB1 loss is associated with clinical resistance to CDK4/6 inhibitors•Knockout of FAT1 causes Hippo pathway suppression in ER+ cancers•YAP/TAZ nuclear localization induces CDK6 overexpression•Genomic alterations causing YAP activation lead to CDK6-mediated resistance Li et al. identify inactivation of RB1 and FAT1 to be associated with resistance of ER+ breast cancer to CDK4/6 inhibitors (CDK4/6i). FAT1 loss increases CDK6 expression via the Hippo pathway. Inactivation of the Hippo pathway component NF2 also increases CDK6 expression and reduces sensitivity to CDK4/6i.