Seems like you are having some issue with your muscles of the neck and upper back,mainly trapezius and lavetar scapulae, that causes headaches too. Your work profile might be of long sitting and mostly in front of the desktop all day, that is why it is increasing by the end of the day.
Next Steps
Please do consult a Physiotherapist. You might have trigger points in the areas of neck and upper back. They will assess and release them so that you are pain free. consult a manual Physiotherapist.
Health Tips
Try using a Towel roll under your neck instead of pillow.
also few stretches of the neck.
Tkcre.