A chordate animal having protonephridia as excretory structure is

Flatworms, rotifers and Amphioxus have protonephridia for osmoreguation and excretion. 

Amphioxus is a chordate (cephalochordate). It has protonephridia with solenocytes as the terminal cells.

In nonchordates, (flatworms and rotifers) protonephridia possess flame cells.

Nephridia are the excretory structures of earthworms.