On the morning of Sunday 29th March the two armies were deployed facing each other; the Yorkists facing north with the village of Saxton at their back, the Lancastrians facing south with Towton behind them. The land between the two villages rises gently from the flat moor in the east to a height of about 150ft, but then falls sharply from a scarp on the west, along the bottom of which runs the Cock Beck. Midway along this ridge an east-west valley called Towton Dale cuts across, gently sloping in the east but dropping more sharply into the Cock valley on its western edge. It was on opposing sides of Towton Dale that the two armies were deployed.

Edward was present on the field and took command of the Yorkist army. The Lancastrian army was commanded by the Duke of Somerset and it is uncertain if Henry was present. At about nine in the morning as the battle began with an arrowstorm from the Yorkist lines, snow began to fall blowing from the south. The Lancastrians returned fire but their view, and therefore their aim, was hampered by the snow that whirled in their faces. The Lancastrian arrows fell short but unaware of this in the blinding snow they continued to fire until their arrows were exhausted. The Yorkists now advanced and collected some of the fallen arrows of their enemies, then, giving insult to injury, returned them with far greater accuracy. The Lancastrians now attacked and had some initial success with their cavalry on their right flank. The Yorkist cavalry on the western side of the battle field broke and fled, but Edward was able to contain the danger and exhort his troops to greater efforts.

The main bodies of the two armies now meet in a bloody clash of hand-to-hand fighting. Details for the course of the battle are scarce, in spite of the fact that it is reported to have lasted for ten hours. However, such sources as there are agree that the mêlée that ensued was vicious and prolonged. The arrival of the delayed Yorkists troops, under the Duke of Norfolk, at about noon though undoubtedly of significant advantage did not have an immediate effect on the course of the battle. Gradually the Lancastrians were pushed back their ranks disintegrating into disorganised groups. As panic spread they fled to the ford of the Cock at Tadcaster. The Yorkists were not prepared to let them go and at the bottleneck of the ford some of the greatest slaughter of the day took place.

Henry, Margaret, the Prince of Wales and Somerset fled to Scotland. After triumphantly entering York the day after the battle Edward retuned to London to prepare for his coronation.