Flamininus, with his allies from the Aetolian League, was stationed at Thebes, and marched out towards Pherae in search of Philip, who was at Larisa. When Flamininus began his march to Larisa he had under his command about 32,500 to 33,400 soldiers. Besides the usual Roman troops and auxiliary units that would appear in any Roman army Flamininus's forces also included soldiers from the allied Aetolian League, light infantry from Athamania, mercenary archers from Crete, and elephants and Numidian cavalry from King Masinissa of Numidia. Philip had about 16,000 heavy infantry in phalanx formation, 2,000 peltasts, 5,500 light infantry from Illyria, Thrace, and Crete, and 2,000 cavalry for 25,500 troops overall. The two armies met near Pherae, and Philip's troops were defeated in a cavalry skirmish on the hills outside the city. Both sides then marched toward Scotusa in search of food, but out of sight of each other because of the hills.
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, ending up on the Cynoscephalae hills. Flamininus sent out his cavalry, which engaged Philip's troops when they unexpectedly came upon the Macedonian camp. Flamininus sent 500 cavalry and 2,000 infantry as reinforcements, forcing Philip to withdraw further up the hill. The commander of Philip's mercenaries, Athenagoras, chased the Romans off the hill, and, having been told that they were fleeing in disorder, Philip reluctantly decided to move his troops, some 8,000 phalangites, into the field below the hill.
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 of light infantry against Philip. Flamininus joined with the reinforcements he had sent ahead earlier, and came up against the phalanx making up Philip's right wing. After the phalanx had repulsed the legions the first time, and forced them to withraw to rougher terrain, where it was hard for the phalanx to operate with their long spears, Philip had his pezhetairoi throw away their spears and fight with their swords. He repositioned his troops so that the line was twice as deep, and placed the cavalry and light infantry on the right wing.
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 position, so they had not even formed the phalanx yet, and Flamininus sent his elephants charging into them, routing them completely. 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, although without their long spears, were still in phalanx formation and 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 soon fled.
After a brief pursuit, Flamininus allowed Philip to escape. According to Polybius and Livy, 5,000 Macedonians had been killed (although Livy states that other sources claim 32,000 Macedonians were killed). Flamininus also took 1,000 prisoners. The Romans lost about 2,000 men.
This Macedonian defeat marks the passing of imperial power from the successors of Alexander the Great to Rome. Along with the later Battle of Pydna, this defeat is often held to have demonstrated that the Macedonian phalanx, formerly the most effective fighting unit in the ancient world, was now obsolete, although in fact the phalanx was able to force the legions back and held their own with swords until twenty maniples fell upon their rear (due to the weak Macedonian flanks and the Roman elephants routing the disordered Macedonian left flank). In Alexander's day the phalanx had been given strong flank guards and significant cavalry forces to do much of the attacking, but in the intervening centuries these practices had been abandoned, leaving the phalanx vulnerable in the flanks. Although the peace that followed allowed Philip to keep his kingdom intact as a buffer state between Greece and Illyria, Flamininus proclaimed that the Greek states formerly under Macedonian domination were now free. Philip also had to pay 1,000 talents to Rome, as well as disband his navy and most of his army. He also had to send his son to Rome as a hostage.