Yes it will work. The 99-00 EX or Si engine harness is the easiest harness to use if you are installing a VTEC motor into any 99-00 EK Civic. Depending on the motor - B16A2, B18C1, etc. you will at the least have to extend or reroute a few plugs and add a wire or 2. This is the easiest and best harness to go with to simplify the wiring, especially if you have a nonVTEC car like a DX or CX.