Are you using Feature EventReviever to add and configure the Job in Job Definitions?

This will add the job in Jobs Definition Section and Deactivating Feature will Remove the Job if you activate the Feature.
public override void FeatureActivated(SPFeatureReceiverProperties properties)
    {
        try
        {
            SPSecurity.RunWithElevatedPrivileges(delegate ()
            {
                SPWebApplication parentWebApp = (SPWebApplication)properties.Feature.Parent;
                DeleteExistingJob(JobName, parentWebApp);
                CreateJob(parentWebApp);
            });
        }
        catch (Exception ex)
        {
            throw ex;
        }
    }
public override void FeatureDeactivating(SPFeatureReceiverProperties properties)
    {
        lock (this)
        {
            try
            {
                SPSecurity.RunWithElevatedPrivileges(delegate ()
                {
                    SPWebApplication parentWebApp = (SPWebApplication)properties.Feature.Parent;
                    DeleteExistingJob(JobName, parentWebApp);
                });
            }
            catch (Exception ex)
            {
                throw ex;
            }
        }
    }
If this is not the issue and you have a Feature Event Reciever then share the cs file here.