Significance A potential avenue to control the spread of mosquito disease vectors lies in reproductive events that follow a blood meal. A key component is the massive production of yolk proteins in the fat body tissue, governed by regulatory networks triggered by the available nutrients. MicroRNAs play a critical role in mosquito egg maturation, and deciphering their dynamics and targets is necessary to fully realize these regulatory processes. We carried out a tissue-specific and time-resolved characterization of microRNA expression in the Aedes aegypti fat body and integrated these results with transcriptome-wide determination of their mRNA targets, followed by validation. This extensive analysis lays the groundwork for a systemic understanding of the gene regulation that underpins reproductive events in the female mosquito.