A Secure Store application is a way to impersonate a specific group or user, so that your application can refer to the Application and use it for authentication. Here are the basics on how to create one.

• Open Central Admin.
• Under ‘Application Management’, you’ll find a link that says ‘Manage service applications’ – click the link.
• Scroll down to find ‘Secure Store Service’ – click on that link
• Click on the ‘New’ icon in the Edit Ribbon tab. (you might need to Generate a New ‘Key’, if it hasn’t already been done. Just look in the ribbon, click the button and remember/store the Pass Phrase you enter.)
• Give it a ‘Target Application ID’, ‘Display Name’ and ‘Contact Email’ address.
• Next choose your ‘Target Application Type’. As it says on the screen, to the left, “The Target Application page URL can be used to set the values for the credential fields for the Target Application by individual users”. The ID and name can be anything you want it to be. It does not designate a specific SharePoint or ASP.Net application. ‘Individual’ and ‘Group’ are the most common selections needed.
• Click the ‘Next’ button
• Click the ‘Next’ button again, even though you will be revisiting this page. If you create credentials at this point, there is a chance, when editing, that the credentials might show in clear text.
• On this page, you will set up the Application Administrators and Members (The users and groups that are mapped to the credentials defined for this Target Application). Once this is set up, click the ‘OK’ button.

And there you go!