The movie opens in 48 B.C. shortly after the Battle of Pharsalus where Julius Caesar (Rex Harrison) has defeated Pompey's army in a brutal civil war for control of the Roman Republic. Caesar learns that Pompey has fled to netrual Egypt, hoping to enlist the support of the young teenage Pharaoh Ptolemy XIII (Richard O'Sullivan) and his sister Cleopatra (Elizabeth Taylor).
A few months later, Caesar arrives in Alexandria, the then-capital of Egypt. He meets the teenage Ptolemy whom is frequently surrounced by an entourage of ministers and advisers, who seem to do most of the thinking and decision-making for him. As a gesture of 'goodwill', the Egyptians present Caesar with Pompey's severed head, but Caesar is not pleased; it is a sorry end for a worthy foe.
As Caesar settles in at the palace, Apollodorus (Cesare Danova), disguised as a rug peddler, brings a gift from Cleopatra. When a suspicious Caesar unrolls the rug, he finds Cleopatra herself concealed within. He is intrigued with the young queen's beauty and warm personality as she persuades him to help her take back her thrown from her younger brother.
Days later, Cleopatra warns Caesar that her brother has surrounded the palace with his soldiers and that he is vastly outnumbered. Caesar is unconcerned. He orders the Egyptian fleet burned so he can gain control of the harbor. The fire spreads to the city, burning many buildings, including the famous Library of Alexandria. Cleopatra angrily confronts Caesar, but he refuses to pull troops away from the fight with Ptolemy's forces to deal with the fire. In the middle of their spat, Caesar begins kissing her.
The Romans hold the main gate to the city after a fierce nightime battle. The next day, the armies of Mithridates arrive on Egyptian soil and drive off the armies of Ptolemy. The following day, Caesar passes judgment in a show trial. He sentences Ptolemy's lord chamberlain to death for arranging an assassination attempt on Cleopatra, and rules that Ptolemy and his tutor be bannished to the desert to join Ptolemy's now greatly outnumbered troops, a sentence of death as the Egyptian army faces off against the Mithridates.
Cleopatra is crowned Queen of Egypt. Afterwords, she tells him about her dreams of ruling the world with Caesar. A year later, a pregnant Cleopatra gives birth to their son Caesarion. Caesar accepts him publicly, which becomes the talk of Rome and the Senate.
Caesar returns to Rome for his triumph, while Cleopatra remains in Egypt. Two years pass before the two see each other again. After he is made dictator for life, Caesar sends for Cleopatra. She arrives in Rome in a lavish procession and wins the adulation of the Roman people. The Roman Senate grows increasingly discontented amid rumors that Caesar wishes to be made king, which is anathema to the Romans.
On the Ides of March in 44 B.C., the Senate is preparing to vote on whether to award Caesar additional powers for the Republic. Despite warnings from his wife Calpurnia (Gwen Watford) and Cleopatra, he is confident of victory. However, he is stabbed to death by various senators.
Octavian (Roddy McDowall), Caesar's nephew, is named as his heir, not Caesarion. Realizing she has no future in Rome, Cleopatra returns home to Egypt.
Two years later in 42 B.C., Caesar's assassins, among them Cassius (John Hoyt) and Brutus (Kenneth Haigh), are killed at the Battle of Philippi. Marc Antony (Richard Burton) establishes a Second Triumvirate goverment with Octavian and Lepidus. They split up the empire: Lepidus receives Africa, Octavian Spain and Gaul, while Antony will take control of the eastern provinces including Asia Minor and Syria. However, the rivalry between Octavian and Antony is becoming apparent.
In 38 B.C., while planning a campaign against Parthia in the east, Antony realizes he needs money and supplies, and cannot get enough from anywhere but Egypt. After refusing several times to leave Egypt, Cleopatra gives in and meets him in Tarsus. Antony becomes drunk during a lavish feast aboard Cleopatra's large golden ship. Cleopatra sneaks away, leaving a slave dressed as her, but Antony discovers the trick and confronts the queen in her bed chaimber. They soon become lovers.
Octavian uses their affair in his smear campaign against Antony. When Antony returns to Rome to address the situation brewing there, Octavian traps him into a marriage of state to Octavian's sister, Octavia (Jean Marsh). Cleopatra flies into a rage when she learns the news.
A year or so later, when Antony next sees Cleopatra, he is forced to humble himself publicly. She demands a third of the Roman empire in return for her aid. Antony acquiesces and divorces Octavia. Octavian clamors for war against Antony and his "Egyptian whore". The Senate is unmoved by his demands until Octavian reveals that Antony has left a will stating that he is to be buried in Egypt; shocked and insulted, the Senators who had previously stood by Antony abandon their hero and vote for war. Octavian murders the Egyptian ambassador, Cleopatra's tutor Sosigenes (Hume Cronyn), on the Senate steps.
The war is decided at the naval Battle of Actium on September 2, 31 B.C. where Octavian's battle fleet, led by General Agrippa (Andrew Keir) lures the overconfident Antony's ships away from land and defeats them in piecemeal. Seeing Antony's ship burning, Cleopatra assumes he is dead and orders the Egyptian forces home. Antony follows, leaving his fleet leaderless and soon defeated.
Several months later, Cleopatra manages to convince Antony to retake command of his troops and fight Octavian and Agrippa's advancing army. However, Antony's soldiers have lost faith in him and abandon him during the night. Rufio (Martin Landau), the last man loyal to Antony, is killed. Antony tries to goad Octavian into single combat, but is finally forced to flee to Alexandria.
When Antony returns to the palace, Apollodorus, not believing that Antony is worthy of his queen, convinces him that she is dead, whereupon Antony falls on his own sword. Apollodorus then takes Antony to Cleopatra, and he dies in her arms. Octavian captures the city without a battle and Cleopatra is brought before him. He wants to return to Rome in triumph, with her as his prisoner. However, realizing that her son is also dead, she arranges to be bitten by a poisonous asp. In the final shot, Octavian and Agrippa enter Cleopatra's temple afterwords to see her dead, dressed in a gold funeral robe with her two handmaidens, also bitten by the same venomous snake that Cleopatra allowed herself to get bitten, dying by her side. Octavian also finds a last letter from Cleopatra requesting to be buried with Marc Antony.
In the voice-over epilogue, the narrator claims that Octavian accepted Cleopatra's last request and allowed her to be buried with full honors next to Marc Antony inside her palace in Alexandria. Octavian returned to Rome several months later in to a hero's welcome for ending the last Roman civil war, and two years later, Octavian adopted the name Augustus and proclaimed himself emperor of the newly formed Roman Empire, and Egypt became a conqured Roman provence.