A fan expansion card includes a first circuit board and at least one first fan. The first circuit board has at least one through-hole. The first circuit board includes a first connection port having a PCI-E interface. Each of the first fans is disposed at a position on the first circuit board corresponding to the through-hole. The first fan is electrically connected to the first circuit board, wherein an airflow generated by each of the first fans passes through the corresponding through-hole. A motherboard module having the above fan expansion card is further provided.