During the march there was a heavy rainstorm, and the morning after there was a fog over the hills and fields separating both camps. Despite this, Philip resumed his march, and his troops became confused and disoriented. Philip then sent a small force to take the Cynoscephalae hills. Flamininus, still unaware of Philip's location, sent out some cavalry and light infantry to reconnoiter, which engaged Philip's troops on the hills. The battle on the hills grew fierce and Flamininus sent 500 cavalry and 2,000 infantry as reinforcements, mostly Aetolians, forcing Philip's men to withdraw further up the hill. Philip now sent more men into the melee, his Macedonian and Thessalian horse, who drove the Romans down the hill, until the Aetolian cavalry stabilized the situation. Philip, though reluctant to send his phalanx into the broken, hilly terrain eventually ordered an assault with 8,000 men when he heard of the Roman retreat. Flamininus positioned his troops on the field as well. He left his right wing in reserve, with his elephants in front, and personally led the left wing against Philip. Meanwhile Philip's phalanx had reached the summit, and after joining with their light troops and cavalry which he placed on his right wing, Philip had his phalanx charge down the hill into the oncoming legionaries. As the Roman left was slowly being driven back, Flamininus took command of his right and ordered an assault there.

Philip's right wing was now on higher ground than the Roman left, and was at first successful against them. His left wing and center, made up of another 8,000 phalangites, however were still disorganized and in marching formation, so they had not even formed the phalanx yet, and as Flamininus sent his elephants charging into them, they routed. After breaking through, one of the Roman tribunes took twenty maniples (a smaller division of the legion) and attacked the Macedonian right wing from behind. The Macedonians were unable to reposition themselves as quickly as the Roman maniples. Now surrounded by both wings of the Roman legion, they suffered heavy casualties and fled.