Aedes aegypti mosquitoes are the primary vector of disease‐causing viruses such as yellow fever, Zika, dengue fever, and chikungunya. With increasing insecticide resistance, novel control approaches informed by an improved understanding of mosquito biology are urgently needed to reduce vector‐borne disease transmission. Our research aims to further understand the molecular and physiological mechanisms that underlie mosquito‐host interactions. Female mosquitoes feed on warm‐blooded vertebrate hosts to obtain blood nutrients required for egg development, but are subjected to extreme thermal stress when feeding and, upon digestion of the blood, must cope with high levels of oxidative stress. Increased knowledge of the biological mechanisms mosquitoes use to cope with these stressors may have important epidemiological consequences for humans. Using next‐generation sequencing methods, we have characterized rhythmic daily variations in the global transcriptome of female Ae. aegypti heads, which encompass the visual and olfactory sensory appendages mosquitoes rely on to sense host‐seeking cues, the mouthparts, and tissues immediately exposed to blood stressors when feeding. Here we describe daily rhythms in mosquito host‐seeking and blood‐feeding stress tolerance. We also investigated daily rhythms in the metabolism of blood digestion, as these mechanisms represent targets of opportunity for mosquito control. Using state‐of‐the‐art respirometry methods to quantify rhythms in the metabolism of blood digestion in female Ae. aegypti mosquitoes, we were able to observe individual ventilatory patterns and compare the metabolic rates at rest and during digestion. These are the first measurements reported on carbon dioxide release from individual Ae. aegypti female mosquitoes and, thus, these results provide new insights regarding mosquito respiratory and metabolic physiology. Analysis of the metabolic rate following the ingestion of various diets additionally allows us to evaluate the effects of diet composition, oxidative stress exposure, and blood protein digestion on mosquito metabolism. Since this work can be used to identify novel vector control approaches targeting mosquito blood meal processing, our results will inform future efforts to decrease mosquito‐borne disease. Support or Funding Information USDA National Institute of Food and Agriculture, Hatch project 1017860. The Company of Biologists Journal of Experimental Biology Travelling Fellowship.