If you use part of your home for business, you may be able to deduct expenses for the business use of your home.
When S-corporation reimburse you as an employee of said S-corporation for use of your home - you need to provide adequate report to the S-corporation about all your business related expenses including business use of your home.
Please be aware about new Simplified Option available for taxable years starting on, or after, January 1, 2013 (filed beginning in 2014) - you now have a simpler option for computing the business use of your home (IRS
Revenue Procedure 2013-13, January 15, 2013). The standard method has some calculation, allocation, and substantiation requirements that are complex and burdensome for small business owners. This new simplified option can significantly reduce record keeping burden
by allowing a qualified taxpayer to multiply a prescribed rate
by the allowable square footage of the office in lieu of determining actual expenses.
I mentioned above a new Simplified method that you may use starting this year - if you choose so - no need to calculate depreciation or any other actual expenses. The new optional deduction, capped at $1,500 per year based on $5 a square foot for up to 300 square feet.
In this case - you do not need to claim depreciation and will not need to recapture the depreciation when you sell your home.