The incident happened at 5:40 a.m. on Saturday near North Pacific Avenue and Broadway, the California Highway Patrol reported.
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The officer was responding to a call when he struck the pedestrian, who has since been identified as 45-year-old Derrick Deon Flanders of Rancho Palos Verdes.
CHP said Flanders was taken to the hospital after the crash where he later died.
No officers were injured.
Investigators are still trying to determine the circumstances that led up to the crash.
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The officer was driving a Ford Explorer belonging to the Huntington Beach Police Department, according to a CHP report.
The CHP is investigating the crash because a city of Huntington Beach vehicle is involved, authorities said.
Anyone who may have witnessed the crash is urged to contact the CHP Westminster office at 714-892-4426.