Trastuzumab is the only approved targeted drug for first-line treatment of human epidermal growth factor receptor 2 (HER2)-positive advanced gastric cancer (GC), but the high rate of primary resistance and rapid emergence of secondary resistance limit its clinical benefits. We found that trastuzumab-resistant (TR) GC cells exhibited high glycolytic activity, which was controlled by hexokinase 2 (HK2)-dependent glycolysis with a circadian pattern (higher at zeitgeber time 6, lower at zeitgeber time 18). Mechanistically, HK2 circadian oscillation was regulated by a transcriptional complex composed of peroxisome proliferator-activated receptor γ (PPARγ) and the core clock gene PER1. In vivo and in vitro experiments demonstrated that silencing PER1 disrupted the circadian rhythm of PER1-HK2 and reversed trastuzumab resistance. Moreover, metformin, which inhibits glycolysis and PER1, combined with trastuzumab at zeitgeber time 6 significantly improved trastuzumab efficacy in GC. Collectively, these data introduce the circadian clock into trastuzumab therapy and propose a potentially effective chronotherapy strategy to reverse trastuzumab resistance in GC.