To figure the cost of absenteeism per employee simply divide the total cost by total number of employees and you see a $1,387 cost per employee each year. Studies find that an employee wellness program can decrease absenteeism by as much as 17.5% or $243 per employee, per year.o figure the cost of absenteeism per employee simply divide the total cost by total number of employees and you see a $1,387 cost per employee each year. Studies find that an employee wellness program can decrease absenteeism by as much as 17.5% or $243 per employee, per year.