A configuration information writing apparatus for writing configuration information defining a logical configuration of a logic circuit device into the logic circuit device to change the logical configuration thereof, the apparatus comprising: a difference extracting unit that acquires plural pieces of configuration information and extracts differences between each of the acquired plural pieces of configuration information; a differential relation generating unit that generates a differential relation indicating a relation of the differences between each of the plural pieces of configuration information based on the differences extracted by the difference extracting unit; and an order information generating unit that generates order information specifying an order of writing the configuration information from the relation of the differences indicated by the differential relation generated by the differential relation generating unit.