Ceramides increase during obesity and promote insulin resistance. Ceramides vary in acyl-chain lengths from C_14:0 to C_30:0 and are synthesized by six ceramide synthase enzymes (CerS1–6). It remains unresolved whether obesity-associated alterations of specific CerSs and their defined acyl-chain length ceramides contribute to the manifestation of metabolic diseases. Here we reveal that CERS6 mRNA expression and C_16:0 ceramides are elevated in adipose tissue of obese humans, and increased CERS6 expression correlates with insulin resistance. Conversely, CerS6-deficient (CerS6^Δ/Δ) mice exhibit reduced C_16:0 ceramides and are protected from high-fat-diet-induced obesity and glucose intolerance. CerS6 deletion increases energy expenditure and improves glucose tolerance, not only in CerS6^Δ/Δ mice, but also in brown adipose tissue- (CerS6^ΔBAT) and liver-specific (CerS6^ΔLIVER) CerS6 knockout mice. CerS6 deficiency increases lipid utilization in BAT and liver. These experiments highlight CerS6 inhibition as a specific approach for the treatment of obesity and type 2 diabetes mellitus, circumventing the side effects of global ceramide synthesis inhibition.