To delete a course, you must either be an administrator or a privileged employee (Manage Course/Batch privilege must be provided). 

Note: You cannot delete a course that contains batches, students, subjects and examination (Kindly check if examination is created in both Gradebook and examination Module). In-order to delete the course you have to remove the Examination, students, subjects and the batches associated with the course and then delete the course.

At the top of your dashboard, click the menu > 
Administration > Settings > Manage Course/Batch > Manage Course to open the Manage Course page.
  1. Click Delete beside the course you want to delete.

                                                                         Fig 1.

  1. Click OK to confirm.   

For more information, watch this-