How much does it cost to replace ductwork in a story home? We are replacing it because we are buying the home and want a fresh start with the duct work. We are also going to get a clean and sanitizing of the furnace and all vents..Air Duct Cleaning Cost. The average cost of duct cleaning is $, or between $ and $. The size of your ductwork, degree of contamination and ease of access affect the price. Cleaning your ducts every years, or more, can improve the energy efficiency and air quality in your home..Shop our selection of Flexible Ductwork in the Heating, Venting Cooling Department at The Home Depot..In general, this sort of work costs between $, $, at minimum and, in especially challenging or large homes, can cost upwards of $, or more. The installation of ducting can seem like a huge and overwhelming job..