Like most of the oases there is not much information about Kharga during Pharaonic times. The oases were hard to subdue due to their distance from the Nile and the difficulty of the journey to reach them. Pottery found recently on the route from Luxor dates from the Middle Kingdom –over 3000 years ago. The most evidence of habitation is from the Roman times. At any time the Romans had about 1000 men based around Kharga. They built new wells, temples and a string of fortresses along the caravan routes. They also used Kharga as a place to exile troublemakers to. Juvenal was a famous Roman exile and the practice was continued after the Romans left. Christians, among them Athanasius, the Bishop of Alexandria, and Bishop Nestorius were also banished to Kharga. The large Christian cemetery- Bagawat- clearly shows that Kharga was completely Christian for several hundred years until the Arabs reached the oasis in the C7th A.D. During this Christian period some of the old temples and forts were converted to churches and monasteries were established.

Overseeing the caravan routes remained an important priority until very recently. Travellers passing through commented on the well-maintained wells. The only north-south route is the Darb al-Arbein. It was a notoriously harsh slave route from Sudan and was also used to carry salt. Going east-west are the Darb al-Ghubari, the Dust Road, and the Darb Ain Amur, known as the Road of the Lovely One. Both roads connected Kharga and Dakhla but the Dust Road was the more difficult route as it was waterless.

By the C19th European visitors were common. Cailliaud travelled to Kharga as well as the other oases. He rediscovered the forgotten Temple of Hibis. Other travellers included Sir Archibald Edmondstone, the French consul Drovetti and George Hoskins who also provided valuable illustrations of the oasis. Their accounts provide details that the women of Kharga appeared to have a lot of influence over their husbands, were often in charge of the family's money and did not cover their faces as in other oases. The ubiquitous Rohlfs also visited Kharga but did not stay long. He was followed in the 1890s by Hugh Beadnell and John Ball who mapped the oasis for the Geological Society. Under British Occupation Kharga slowly became a tourist destination. Trains opened the oasis up to greater contact with the Nile Valley.

Recent History
After World War 2 the oases all suffered a time of deprivation. It wasn't until 1958 that Gamal Abdel Nasser created the New Valley region (Wadi al-Jadid). The oases of Kharga, Dakhla and Farafra were linked under one authority. The road to Asyut was paved, an airport was built and the area expanded rapidly. Wells were cleaned, the High Dam was opened and the amount of cultivable land increased dramatically. Agriculture increased. Villages now receive electricity and hospitals and schools are more widespread. Tourism is a most important element of the New Valley's regeneration.