Medaka Oryzias latipes is a well-recognized biomedical fish model because of advantageous features such as small body size, transparency of embryos, and established techniques for gene knockout and modification. The goal of this study was to evaluate two critical factors, cryoprotectant and cooling rate, for sperm cryopreservation in 0.25-ml French straws. The objectives were to: (1) evaluate the acute toxicity of methanol, 2-methoxyethanol (ME), dimethyl sulfoxide (Me(2)SO), N,N-dimethylacetamide (DMA), N,N-dimethyl formamide (DMF), and glycerol with concentrations of 5%, 10%, and 15% for 60min of incubation at 4°C; (2) evaluate cooling rates from 5 to 25°C/min for freezing and their interaction with cryoprotectants, and (3) test fertility of thawed sperm cryopreserved with selected cryoprotectants and associated cooling rates. Evaluation of cryoprotectant toxicity showed that methanol and ME (5% and 10%) did not change the sperm motility after 30min; Me(2)SO, DMA, and DMF (10% and 15%) and glycerol (5%, 10% and 15%) significantly decreased the motility of sperm within 1min after mixing. Based on these results, methanol and ME were selected as cryoprotectants (10%) to evaluate with different cooling rates (from 5 to 25°C/min) and were compared to Me(2)SO and DMF (10%) (based on their use as cryoprotectants in previous publications). Post-thaw motility was affected by cryoprotectant, cooling rate, and their interaction (P⩽0.000). The highest post-thaw motility (50±10%) was observed at a cooling rate of 10°C/min with methanol as cryoprotectant. Comparable post-thaw motility (37±12%) was obtained at a cooling rate of 15°C/min with ME as cryoprotectant. With DMF, post-thaw motility at all cooling rates was ⩽10% which was significantly lower than that of methanol and ME. With Me(2)SO, post-thaw motilities were less than 1% at all cooling rates, and significantly lower compared to the other three cryoprotectants (P⩽0.000). When sperm from individual males were cryopreserved with 10% methanol at a cooling rate of 10°C/min and 10% ME with a rate of 15°C/min, no difference was found in post-thaw motility. Fertility testing of thawed sperm cryopreserved with 10% methanol at a rate of 10°C/min showed average hatching of 70±30% which was comparable to that of fresh sperm (86±15%). Overall, this study established a baseline for high-throughput sperm cryopreservation of medaka provides an outline for protocol standardization and use of automated processing equipment in the future.