The standard mileage rate for 2016 is 54 cents, so you are entitled to deduct the difference.  After you enter the information for your mileage deduction, you'll enter the amount you were reimbursed.  Please go to Federal Income>Deductions & Credits>Job-Related Expenses to enter this deduction.

Please keep in mind that your job-related expenses and other miscellaneous deductions must be more than 2% of your AGI (adjusted gross income) to be deductible.  Example: If your AGI is $40,000, your miscellaneous deductions would have to be more than $800 ($40,000 x 2%). Even then, you could only deduct the amount over $800. So, if your miscellaneous deductions were $1,000 you could only deduct $200 ($1,000 - $800).