Yes, it may take some time, but if you overpaid the IRS with a direct payment from your bank, they will return the money to you.
Once they match up the overpayment with your tax return, they will mail a paper check and letter showing the overpayment on your account.
You can also try contacting them at (800)829-1040; however, it is very difficult to get through to them at the height of tax season.
In addition, you can use this IRS link to access your account information: https://www.irs.gov/payments/view-your-tax-account.
