I have had hypothyroidism for the past 5 years now and recently i am having this burning sensation on my head which is very uncomfortable.

Probably not related: Hard to know what this is - suggest see a doctor. Not a typical symptom of hypothyroidism - see the link below. Best to get yourself assessed and examined. http://patient.info/health/underactive-thyroid-gland-hypothyroidism

Hypothyroidism: your burning sensation may not be related to hypothyroidism.Pts with hypothyroidism tend to have low B12 especially if they have dietary restriction.I would recommend to have your B12 levels checked and take B12 supplements to see if it helps burning sensation

Headache hypothyroid: Hypothyroid 5 years now headache. ANS: very unlikely these are related. Keep a headache diary and discuss with Dr.