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Adolescence and emerging adulthood is likely a sensitive period for the neural effects of stress due to increasing life stress, onset of stress-related disorders, and continued gray matter (GM) development. In adults, stress is associated with GM differences in the medial prefrontal cortex (mPFC), hippocampus, and amygdala, but little is known about these relations, and whether they differ by gender, during adolescence and emerging adulthood. Further, it is unknown whether dependent (self-generated) and independent (fateful) stressors have distinct associations with GM, as each have distinct relations with internalizing psychopathology. We tested relations between recent dependent and independent stressor frequency (ALEQ-R) and GM structure using MRI in a priori regions of interest (mPFC, amygdala, and hippocampus) and across the cortex in youth from the Denver/Boulder metro area ages 14-22 (N = 144). Across both genders, no effects passed multiple comparison correction (FDR q > 0.05). However, there were significant differences between male and female youth (FDR q < 0.05), with opposite relations between dependent stressor frequency and cortical GM thickness in the salience network and emotion regulation regions and with surface area in default mode network regions. These results motivate future investigations of gender differences in neural mechanisms of stress generation and reactivity.