Different fasting regiments are known to promote health, and chronic immunological disorders and mitigate age-related pathophysiological parameters in animals and humans. Indeed, several clinicals trials are currently ongoing using fasting as a potential therapy for a wide range of conditions. Fasting alters metabolism by acting as a reset for energy homeostasis, but the molecular mechanisms underlying the beneficial effects of short-term fasting (STF) are still not-well understood, particularly at a systems/multiorgan level. We investigated the dynamic gene expression patterns associated with periods of STF in nine different mouse organs. First, we identified both unique and shared transcriptional signatures at the organ and systemic levels. Second, we discovered differential temporal effects of STF among organs. Third, using gene ontology enrichment analysis, we identified an organ network, formed by the 63 common biological pathways perturbed by STF. This network incorporates the brain, liver, interscapular brown, and perigonadal white adipose tissue, hence we name it the brain-liver-fats organ network. Fourth, we identified that the immune system, dominated by T cell regulation processes, is a central and prominent target of systemic modulations during short-term energy loss in this organ network. The changes we identified in specific immune components point to the priming of adaptive immunity and parallel the fine-tuning of innate immune signaling. In conclusion, our study provides a comprehensive multi-organ transcriptomic profiling of mice subjected to multiple periods of STF and added new insights into the molecular modulators involved in the systemic immuno-transcriptomic changes that occur during short-term energy loss.