A substrate transfer apparatus transfers substrates stored in a first substrate storage case, which has support grooves in its inner wall, along the support grooves to substrate storage surfaces included in a second substrate storage case. The substrate transfer apparatus includes a first-substrate-storage-case placement section in which the first substrate storage case is placed, a second-substrate-storage-case placement section in which the second substrate storage case is placed, a substrate transfer mechanism that holds the substrates stored in the first substrate storage case so as to draw out the substrates from the first substrate storage case, and transfers the substrates to a substrate placement section of a substrate placing mechanism, a substrate holding mechanism that holds the substrates placed in the substrate placement section at hold positions, and discharges the substrates at discharge positions so as to dispose the substrates on the substrate storage surfaces of the second substrate storage case, and a transport mechanism that transports the substrate holding mechanism from the hold positions to the discharge positions.