Eager to take advantage of Julius Caesar's anger toward Ptolemy, Cleopatra had herself smuggled secretly into the palace to meet with Caesar. Plutarch in his "Life of Julius Caesar" gives a vivid description of how she entered past Ptolemy’s guards rolled up in a carpet, that Apollodorus the Sicilian was carrying. She became Caesar’s mistress, and nine months after their first meeting, in 47 BC, Cleopatra gave birth to their son, Ptolemy Caesar, nicknamed Caesarion, which means "little Caesar."
At this point Caesar abandoned his plans to annex Egypt, instead backing Cleopatra's claim to the throne. After a war lasting six months between the party of Ptolemy XIII and the Roman army of Caesar, Ptolemy XIII was drowned in the Nile and Caesar restored Cleopatra to her throne, with another younger brother Ptolemy XIV as her new co-ruler.
Although Cleopatra was 22 years old when they met and Caesar was 52, they became lovers during Caesar’s stay in Egypt between 48 BC and 47 BC. Cleopatra claimed Caesar was the father of her son and wished him to name the boy his heir, but Caesar refused, choosing his grandnephew Octavian instead. During this relationship, it was also rumored that Cleopatra introduced Caesar to her astronomer Sosigenes of Alexandria, who first proposed the idea of leap days and leap years.
Cleopatra, Ptolemy XIV and Caesarion visited Rome in summer 46 BC, where the Egyptian queen resided in one of Caesar's country houses. The relationship between Cleopatra and Caesar was obvious to the Roman people and it was a scandal, because the Roman dictator was already married to Calpurnia Pisonis. But Caesar even erected a golden statue of Cleopatra represented as Isis in the temple of Venus Genetrix (the mythical ancestress of Caesar's family), which was situated at the Forum Julium. The Roman orator Cicero said in his preserved letters that he hated the foreign queen. Cleopatra and her entourage were in Rome when Caesar was assassinated on 15 March, 44 BC. She returned with her relatives to Egypt. When Ptolemy XIV died – allegedly poisoned by his older sister – Cleopatra made Caesarion her co-regent and successor and gave him the epithets Theos Philopator Philometor (= Father- and motherloving God).