Chief operating officer, Travis Auld, said Stuart is very highly regarded in the football industry.
""Stuart was our number one target when replacing John Quinn and we are delighted to be able to get him to the club,"" Auld said.
""He has been at West Coast for eight seasons and in that time they have made the finals six times, played in two Grand Finals and won a Premiership.
""Stuart has been responsible for a fitness program which has seen the Eagles earn a reputation as one of the competition's hardest running, best prepared teams.
""Prior to West Coast, he spent four years as strength and conditioning coach at the AIS.""
Auld said Stuart and his wife are from Melbourne and, with two young children, were keen to come back to Melbourne to be with family.
""Essendon is very lucky to have had the services of John Quinn for the past decade and we are fortunate to be able to secure someone of the calibre of Stuart to replace him,"" Auld said.