The male rider of a blue Honda motorcycle was travelling north near Karnup Road about 1am when he collided with the animal on the road.
The rider suffered serious injuries, including a broken arm and leg and scratches.
He was taken to Royal Perth Hospital. The deer was killed.
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READ NOWPolice are investigating if speed was a factor in the crash.
The 31-year-old man from Kiara will be charged with no authority to drive and will appear in court at a later date.