Background The neural projections from the infralimbic region of the prefrontal cortex (IL) to the amygdala are important for the maintenance of conditioned fear extinction. Neurons in this pathway exhibit a unique pattern of structural plasticity that is sex-dependent, but the relationship between the morphological characteristics of these neurons and successful extinction in males and females is unknown. Methods Using classic cued fear conditioning and extinction paradigm in large cohorts of male and female rats, we identified subpopulations of both sexes that exhibited high (HF) or low (LF) levels of freezing on an extinction retrieval test, representing failed or successful extinction maintenance, respectively. We then combined retrograde tracing with fluorescent intracellular microinjections to perform 3D reconstructions of IL neurons that project to the basolateral amygdala (BLA) in these groups. Results HF/LF males exhibited neuroanatomical distinctions that were not observed in HF vs. LF females. A retrospective analysis of behavior during fear conditioning and extinction revealed that despite no overall sex differences in freezing behavior, HF/LF phenotypes emerged in males during extinction, but in females during fear conditioning, which does not involve IL-BLA neurons. Conclusion Our results suggest that the neural processes underlying successful or failed extinction maintenance may be sex-specific. These findings are not only relevant to future basic research on sex differences in fear conditioning and extinction, but also to exposure-based clinical therapies, which are similar in premise to fear extinction, and which are primarily used to treat disorders that are more common in women than in men.