An on-board fuel separation system includes a supply fuel tank configured to store an input fuel stream; a fuel separator fluidly coupled to the supply fuel tank and configured to separate the input fuel stream into a first fractional fuel stream and a second fractional fuel stream. The fuel separator includes a membrane that includes a plurality of pores sized based on a molecular size of one or more components of the first fractional fuel stream. The system includes a first fractional fuel tank fluidly coupled to the fuel separator to receive the first fractional fuel stream passed through the membrane and defined by a first auto-ignition characteristic value. The system includes a second fractional fuel stream coupled to the fuel separator to receive the second fractional fuel stream from the fuel separator that is defined by a second auto-ignition characteristic value that is different than the first auto-ignition characteristic value.