An apparatus and a method for updating data in an embedded system are provided. The apparatus includes a processor for retrieving new data and a transmission line. The transmission line connects to the processor to receive the new data and transmits the new data to the embedded system. The data of a data area has a end address for the data and a plurality of application programs arranged in order, and the new data includes an application program update. The embedded system executes the following steps: searching for an application program corresponding to the application program update; if the corresponding application program is found, retrieving a first address and a second address of the corresponding application program; obtaining a length value of the corresponding application program from the second address and the end address; writing contents of the data area from the second address to the end address into the data area beginning from the first address; adding the first address to the length value to obtain a third address; and writing the application program update into the data area beginning from the third address.