Environmental stress (nutritive, chemical, electromagnetic and thermal) has been shown to disrupt central nervous system (CNS) development in every model system studied to date. However, empirical linkages between stress, specific targets in the brain, and consequences for behavior have rarely been established. The present study experimentally demonstrates one such linkage by examining the effects of ecologically-relevant thermal stress on development of the Drosophila melanogaster mushroom body (MB), a conserved sensory integration and associative center in the insect brain. We show that a daily hyperthermic episode throughout larval and pupal development (1) severely disrupts MB anatomy by reducing intrinsic Kenyon cell (KC) neuron numbers but has little effect on other brain structures or general anatomy, and (2) greatly impairs associative odor learning in adults, despite having little effect on memory or sensory acuity. Hence, heat stress of ecologically relevant duration and intensity can impair brain development and learning potential.