The increased reports of wild bee declines and annual losses of managed bees pose a significant threat to biodiversity and agricultural productivity. While these losses and declines are likely driven by various factors, the exposure of bees to agrochemicals has raised significant concern due to their ubiquitous use and potential adverse effects. Despite numerous studies suggesting neonicotinoids can negatively affect bees at the behavioral and molecular level, data linking these two factors remains sparse. Here we provide data on the impact of an acute dose of the neonicotinoid thiamethoxam on the flight performance and molecular transcription profiles of foraging honey bees (Apis mellifera). Using a controlled experimental design with tethered flight mills, we measured flight distance, duration, and speed, alongside the expression of genes involved in energy metabolism, hormone regulation, and biosynthesis. Acute thiamethoxam exposure resulted in hyperactive flight behavior but led to significant dysregulation of genes associated with oxidative phosphorylation, indicating potential disruptions in cellular energy production. These molecular changes were particularly evident when bees engaged in flight activities, suggesting that the combined stress of pesticide exposure and physical exertion exacerbates negative outcomes. Our study provides new insights into the molecular mechanisms underlying neonicotinoid-induced impairments in bee physiology that can help understand the potential long-term consequences of xenobiotic exposure on the foraging abilities of bees and ultimately fitness.