Bisphenol-A (BPA), an environmental endocrine disruptor (EED), is used widely in the manufacturing of various plastics. While BPA can have detrimental effects on fertility and reproductive health, the effects of BPA on early ovarian differentiation in mammals remains unclear. Marsupials have undifferentiated gonads at birth, so this study investigated the gross morphology, protein localisation of FOXL2 and FST and the expression profile of key ovarian differentiating genes FOXL2, WNT4,FST, ESR1 and ESR2 every 2 days from the day of birth to day 10 post partum (pp) in the marsupial tammar wallaby. A second group of newborn female pouch young were treated with 50 µg/kg of BPA daily from day 0-10 pp and the morphology and gene expression were examined at day 10 pp. Ovigerous cords in tammar ovaries were first formed between days 2 to 4 pp. FOXL2 localisation became nuclear by day 4 in pre-granulosa cells. FST was initially in the cytoplasm of pre-granulosa cells at day 2 pp, but was then secreted into the extracellular matrix in ovaries by day 10 pp. FOXL2, FST, ESR1 and ESR2 mRNA were upregulated in ovaries around day 2-4 pp, indicating that ovarian differentiation in the tammar begins from day 2-4 pp. Interestingly, BPA treatment from day 0-10 pp blocked the morphological differentiation of the cortex and medulla as well as ovigerous cord formation and downregulated the expression of FST and FOXL2 at day 10 pp.