The complaints came from Taradale, Greenmeadows, Meeanee and Awatoto.
The company has received seven other infringement notices for odour discharges since 1997.
In sentencing, Judge Dickey said it is clear that the odours which emanated from the rendering plant had an adverse effect on the amenity and enjoyment of residents.
"Odour is hard to escape from and hard to ignore," she said.
"Residents living in the vicinity of the plant are entitled to enjoy their properties without that enjoyment being marred by unpleasant smells."
HBRC group manager policy and regulation Katrina Brunton said the fine sends a strong signal to businesses that breaches of their resource consents will not be tolerated.
"Prosecuting a company is one of the strongest signals we can send to discourage others," she said.
"We welcome the $38,500 fine which should serve as a strong deterrent to others."
The council also encouraged anyone experiencing objectionable odours or other pollution matters to call its 24/7 Pollution Hotline on 0800 108 838.