The Taepyeong-dong complex in Seongnam city, south of Seoul, will be cleared over two days and converted into a public park.
About one million dogs are consumed every year and activists have sought to end the custom.
Dog meat was once considered a delicacy in South Korea, but attitudes have changed in recent years.
"This is a historic moment," Korean Animal Rights Advocates (KARA) said in a statement. "It will open the door for more closures of dog meat slaughterhouses across the country, expediting the decline of the overall dog meat industry."
The Taepyeong-dong complex - an important source of meat for restaurants across the country - housed at least six slaughterhouses, holding several hundred animals at a time.