Rupert had left York early in the morning and on reaching Marston Moor deployed his troops in a defensive position on the flat ground. Immediately to the fore, along the ditch marking the southern edge of the moor, running between the villages of Tockwith in the west and Long Marston to the east, he placed musketeers. His force was strengthened later in the day by the addition of 4,000 troops from Newcastle’s Northern royalist army who had marched out belatedly from York, apparently distracted by the abandoned parliamentarian camp where it is said they had spent the morning looting. They only arrived on the field at about 4 o’clock in the afternoon.

With the addition of Newcastle’s troops, Rupert’s force was still 10,000 less than that of his opponents. The Scottish/parliamentarian army, commanded by Alexander Leslie, the Earl of Leven, drew up facing them in open fields on sloping ground, with the right flank against Long Marston and the left against Tockwith. Apart from an artillery exchange and action on the parliamentarian left, where Rupert tried to dislodge Cromwell's cavalry from the rabbit warren, very little happened for some hours. The two sides cautiously watched each other, with both seemingly reluctant to make the first move. By 7 o’clock in the evening the royalists appear to have decided that no action was going to take place until the following day and began to relax their guard; Rupert and Newcastle standing down many of their troops.

Taking advantage of a thunderstorm, without warning the parliamentarian army moved forwards at a rapid pace down onto the moor. The battle archaeology suggests an intense if brief firefight for the ditch line as the two armies met. The ill prepared royalists were at a major disadvantage, but they were not completely overwhelmed.

On the left Cromwell’s cavalry, supported by Scottish horse under David Leslie, made short work of Byron’s horse, which quickly broke and fled. Rupert then brought his reserve of cavalry in to challenge Cromwell, rallying the fleeing troops of Byron as he did so. Cromwell had been wounded in the initial assault and withdrew, being absent briefly from the field but during a critical stage. Rupert’s attack had some initial success, but with the support Leslie's cavalry reserve the push as halted. Fierce fighting ensued with little ground taken or given. But, brave and experienced as the royalist’s were, they were also outnumbered. Most importantly they were now facing in the Ironsides a highly trained, well equipped and highly committed force, unlike the parliamentarian cavalry that Rupert had defeated earlier in the war. Eventually the royalist right wing of cavalry broke and fled.

On the Parliament right wing Sir Thomas Fairfax fared less well. One account suggests that Fairfax’s approach was hampered by ‘a narrow Lane, where they could not march above 3 or 4 in front’ and were picked off piecemeal by Goring’s horse ‘the enemy keeping themselves in a body, and receiving them by threes and foures as they marched out of the Lane’. While Fairfax charged on through the royalist with a small company of cavalry, Goring’s counter attack swept through the unformed parliamentarian cavalry, which was in such a panic that it turned and fled the field, not stopping for over two miles. In their desperation to get away the fleeing cavalry had trampled some of their own infantry who, caught the panic, also fled. Some of Goring’s cavalry pursued the fleeing parliamentarians, others stopped to loot the baggage train on Marston Hill. Goring’s second line swept in for another attack, this time hitting the exposed flank of Lord Fairfax’s infantry. These too were quickly put to flight and, panic being contagious it spread along the line with several thousand foot fleeing the field. Sir Thomas Fairfax’s own troop of horse had not been caught up in the rout but pursued some fleeing royalist cavalry across the moor towards York. Returning to the field later and he had little choice but to ride through the royalist forces to join the parliamentarian left.

In the centre of the field the royalist cavalry and infantry had considerable success, breaking through the parliamentarian line though not routing them, to reach the summit of the hill in the rear. Traditional accounts of the battle have claimed that at this point senior parliamentarian commanders, thinking the battle lost, now left the field towards Tadcaster, the direction in which many of their soldiers were already fleeing. But recent scholarship has debunked this.  Buoyed by the leadership of the Earl of Leven, many of the Scottish regiments stood firm and maintained their ranks, using their pikes to fend-off the royalist cavalry.

While in the centre and right the parliamentarian cause looked desperate, it was on their left that the battle was being won. Cromwell had returned to the field and his wing of cavalry, together with the Eastern Association infantry to his right, swept across the moor in a wide arc, rolling-up the flank of the royalist infantry, which faced renewed attack from the Scottish foot in the centre.  Goring, having believed the battle won, turned and looked down onto the moor to see the victorious parliamentarian forces facing him, where he himself had been deployed at the beginning of the battle. Goring’s troops were now scattered but he rallied what forces he could and returned to engage the Scots and Eastern Association troops. But the royalist were no match for these well ordered horse and foot, and were soon driven-off the field. But not all fled. According to one account a desperate last stand was taken by the Whitecoats, Newcastle’s own infantry regiment, who were said to have retreated to a hedged enclosure where they held out almost to the last man. But in the end this was a futile gesture for the battle had already been lost.