If you have a runny nose in the morning, you need to take a look at the nature of the nasal discharge in order to initially determine what causes it. If the discharge is clear and accompanied by sneezing, it is considered to be caused by allergic rhinitis, which can be treated with nasal spray hormone or, in severe cases, with oral anti-allergy medication. If you have a yellow nasal discharge in the morning and have a headache, it is considered to be caused by sinusitis, and you need to have a CT examination of your sinuses to determine the severity of sinusitis and then choose whether to treat it with medication or surgery. Symptoms.