This paper discusses the effect of chrononutrition on the regulation of circadian rhythms; in particular, that of chocolate on the resynchronization of the human internal biological central and peripheral clocks with the main external synchronizers, light–dark cycle and nutrition-fasting cycle. The desynchronization of internal clocks with external synchronizers, which is so frequent in our modern society due to the tight rhythms imposed by work, social life, and technology, has a negative impact on our psycho-physical performance, well-being, and health. Taking small amounts of chocolate, in the morning at breakfast at the onset of the active phase, helps speed up resynchronization time. The high flavonoid contents in chocolate promote cardioprotection, metabolic regulation, neuroprotection, and neuromodulation with direct actions on brain function, neurogenesis, angiogenesis, and mood. Although the mechanisms of action of chocolate compounds on brain function and mood as well as on the regulation of circadian rhythms have yet to be fully understood, data from the literature currently available seem to agree in suggesting that chocolate intake, in compliance with chrononutrition, could be a strategy to reduce the negative effects of desynchronization. This strategy appears to be easily implemented in different age groups to improve work ability and daily life.