The origins of such a conflict are complex. The primary causes were that Sparta feared the growing power and influence of the Athenian Empire. The Peloponnesian war began after the Persian Wars ended in 449 BCE. The two powers struggled to agree on their respective spheres of influence, absent Persia's influence. This disagreement led to friction and eventually outright war. Additionally, Athens and its ambitions caused increasing instability in Greece.

The profoundly different Athens and Sparta societies were also a significant factor in the war’s outbreak, which also had an ideological aspect. Over time the Athenians, who were the largest maritime power in the Aegean, dominated the Delian League. This era constituted the Golden Age of Athens and was concurrent with Plato, Socrates, and Aristotle's lives.

Gradually, the Athenians began to turn the Delian League into an Empire. Athens used its superior navy to intimidate its allies, and they eventually became mere tributaries of the Athenians. Sparta soon became very suspicious of Athens's growing power. Sparta was the head of the powerful Peloponnesian League, comprised of several large city-states, including Corinth and Thebes. The League was very concerned about the Athenian fleet because it allowed Athens to dominate Greece's seas.

The Spartan strategy during the first war, known as the Archidamian War (431–421 BC) after Sparta's king Archidamus II, was to invade the land surrounding Athens. While this invasion deprived Athenians of the productive land around their city, Athens itself was able to maintain access to the sea, and did not suffer much. Many of the citizens of Attica abandoned their farms and moved inside the Long Walls, which connected Athens to its port of Piraeus. At the end of the first Year of the war, Pericles gave his famous Funeral Oration (431 BC). The Athenian strategy was initially guided by the strategos, or general, Pericles, who advised the Athenians to avoid open battle with the far more numerous and better trained Spartan hoplites, relying instead on the fleet.

After the Battle of Pylos, which resulted in the isolation of over 400 Spartan soldiers on the island of Sphacteria, Sparta sued for peace, and, after arranging an armistice at Pylos by surrendering the ships of the Peloponnesian fleet as security, sent an embassy to Athens to negotiate a settlement. These negotiations, however, proved fruitless, and with the news of their failure the armistice came to an end; the Athenians, however, refused to return the Peloponnesian ships, alleging that assaults had been made against their fortifications during the truce.

The Spartans, under their commander Epitadas, attempted to come to grips with the Athenian hoplites and push their enemies back into the sea, but Demosthenes detailed his lightly armed troops, in companies of about 200 men, to occupy high points and harass the enemy with missile fire whenever they approached. When the Spartans rushed at their tormentors, the light troops, unencumbered by heavy hoplite armor, were easily able to run to safety.

A stalemate took hold for some time, with the Athenians trying unsuccessfully to dislodge the Spartans from their strong positions. At this point, the commander of the Messenian detachment in the Athenian force, Comon, approached Demosthenes and asked that he be given troops with which to move through the seemingly impassable terrain along the island's shore. His request was granted, and Comon led his men into the Spartan rear through a route that had been left unguarded on account of its roughness. When he emerged with his force, the Spartans, in disbelief, abandoned their defenses; the Athenians seized the approaches to the fort, and the Spartan force stood on the brink of annihilation.

At this point, Cleon and Demosthenes declined to push the attack further, preferring to take as many Spartans as they could prisoner. An Athenian herald offered the Spartans a chance to surrender, and the Spartans, throwing down their shields, agreed at last to negotiate.

Of the 440 Spartans who had crossed over to Sphacteria, 292 survived to surrender; of these, 120 were men of the elite Spartiate class. "The outcome," Donald Kagan has observed, "shook the Greek world." Spartans, it had been supposed, would never surrender. Sphacteria had changed the nature of the war.

In the 17th Year of the war, word came to Athens that one of their distant allies in Sicily was under attack from Syracuse. The people of Syracuse were ethnically Dorian (as were the Spartans), while the Athenians, and their ally in Sicilia, were Ionian. The Athenians felt obliged to assist their ally. Following the defeat of the Athenians in Sicily, it was widely believed that the end of the Athenian Empire was at hand. Their treasury was nearly empty, its docks were depleted, and many of the Athenian youth were dead or imprisoned in a foreign land.

From 414 BC, Darius II, ruler of the Achaemenid Empire had started to resent increasing Athenian power in the Aegean and had his satrap Tissaphernes enter into an alliance with Sparta against Athens, which in 412 BC led to the Persian reconquest of the greater part of Ionia.[3] Tissaphernes also helped fund the Peloponnesian fleet.

The overall effect of the war in Greece proper was to replace the Athenian Empire with a Spartan empire. After the battle of Aegospotami, Sparta took over the Athenian empire and kept all of its tribute revenues for itself; Sparta's allies, who had made greater sacrifices for the war effort than had Sparta, got nothing. Although the power of Athens was broken, it made something of a recovery as a result of the Corinthian War and continued to play an active role in Greek politics. Sparta was later humbled by Thebes at the Battle of Leuctra in 371 BC, but the rivalry between Athens and Sparta was brought to an end a few decades later when Philip II of Macedon conquered all of Greece except Sparta, which was later subjugated by Philip's son Alexander in 331 BC.