Isolation of ovarian follicles is a key step in culture systems for large mammalian species, to promote continued growth of follicles beyond the preantral stage in fertility preservation efforts. Still, mechanical isolation methods are user-skill dependent and time consuming, whereas enzymatic strategies carry increased risk of damaging theca cell layers and the basement membranes. Here, we sought to determine the optimal method to rescue domestic cat (Felis catus) early antral and antral stage follicles from ovarian tissue and evaluate the influence of isolation strategy on follicle development, survival, and gene expression during 14 day in vitro culture in alginate hydrogel. Mechanical isolation was compared with 90 min digestion in 0.7 and 1.4 Wünsch units/ml Liberase blendzyme (0.7L and 1.4L, respectively). Mechanical isolation resulted in improved follicle growth and survival, and better antral cavity and theca cell maintenance in vitro, compared with 1.4L (P<0.05), but displayed higher levels of apoptosis after incubation compared with enzymatically isolated follicles. However, differences in follicle growth and survival were not apparent until 7+ days in vitro. Expression of CYP19A1, GDF9, LHR, or VEGF were similar among isolation-strategies. Cultured follicles from all isolation methods displayed reduced StAR expression compared with freshly-isolated follicles obtained mechanically or via 0.7L, suggesting that prolonged culture resulted in loss of theca cell presence and/or function. In sum, early antral and antral stage follicle development in vitro is significantly influenced by isolation strategy, but not necessarily observable in the absence of extended culture. These results indicate additional care must be taken in follicle isolation optimizations for genome rescue and fertility preservation efforts.