A system and method for liquefying a hydrogen gas feed stream uses a pre-cooling refrigerant for pre-cooling the feed stream, where the pre-cooling refrigerant is compressed, cooled and then separated to provide high pressure mixed refrigerant vapor and liquid streams. The high pressure vapor stream is cooled and directed to a cold vapor separator where cold separator liquid and vapor streams are formed. The cold separator vapor stream is cooled and expanded to provide a pre-cool refrigeration stream in a heat exchanger system. The high pressure pre-cooling refrigerant liquid and cold separator liquid streams are cooled and expanded and directed to the pre-cool refrigeration stream. A high pressure primary refrigerant steam, after compression and cooling, is further cooled in the heat exchanger system and then expanded using warm and cold expanders, with the resulting expanded primary refrigerant streams used to liquefy the pre-cooled hydrogen feed stream via heat exchange in the heat exchanger system.