This solution works if you used Model First and do not want to generate a model from the database. (using VS2013, EF6, MVC5)
Open the EDMX file. Right-click and click Update Model from Database. Check only the "Stored Procedures and Functions" and uncheck the two fields at the bottom, except for "Import selected stored procedures and functions into the entity model" (see Figure below)

Note. If you have data annotations, etc., they will be restored and overwritten.
Link: Using stored procedures in the first approach of the Entity Framework model (Part I - Adding a new stored procedure)
Further explanation and details:
"When the Entity data model wizard creates a .edmx file from the database, it creates entries in the warehouse model for each stored procedure in the database. The corresponding entries are added to the conceptual model when creating the import function." How to import a stored procedure (entity data model tools)
It seems you need to update your model from the database in order to use the "Add New> Import Function .." wizard to import stored procedures. Otherwise, it will not appear in the list. If you add them manually, you run the risk of overwriting them. This will happen every time you edit your model. You will need to update this code at any time when you make changes to the model or database (I would save a copy of it).
Here's how you do it when creating a model from a database: EF model first with stored procedures
They also refer to updating the model from the database on this MSDN community support forum: how to add a new stored procedure to an existing .edmx file
This is the only way I found updating stored procedures WITHOUT updating the model.
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