The age of the Sahara has been a matter of some dispute. Several studies of the rocks in the region indicate that the Sahara became established as a climatic desert approximately 2–3 million years ago, an interval that spanned from the late Pliocene to the early Pleistocene Epoch. The discovery of 7-million-year-old dune deposits throughout northern Chad in 2006, however, suggests that the region became arid during the Miocene Epoch (23 million to 5.3 million years ago). Since the Pliocene the Sahara has been subject to short- and medium-term oscillations of drier and more humid conditions. Human activity seems to have contributed to the stability of the desert by increasing surface reflectivity and by reducing evapotranspiration. During the past 7,000 years cattle-based animal husbandry in the desert and along its margins apparently has contributed further to the maintenance of these conditions, and the climate of the Sahara has been relatively constant for 2,000 years. A noteworthy departure from existing norms occurred from the 16th to the 18th century, the period of the so-called Little Ice Age in Europe: precipitation increased significantly along the tropical margin of the Sahara, in the desert itself, and perhaps along the northern margin as well. By the 19th century, however, a climate similar to that of the present was reestablished.

The Sahara is dominated by two climatic regimes: a dry subtropical climate in the north and a dry tropical climate in the south. The dry subtropical climate is characterized by unusually high annual and diurnal temperature ranges, cold to cool winters and hot summers, and two precipitation maximums. The dry tropical climate is characterized by a strong annual temperature cycle following the declination of the sun; mild, dry winters; and a hot dry season preceding variable summer rains. A narrow strip of the western coastal zone has a relatively cool, uniform temperature reflecting the influence of the cold Canary Current.

The dry subtropical climate of the northern Sahara is caused by stable high-pressure cells centred over the Tropic of Cancer. The annual range of average daily temperatures is about 36 °F (20 °C). Winters are relatively cold in the northern regions and cool in the central Sahara. For the zone as a whole, average monthly temperatures during the cold season are approximately 55 °F (13 °C). The summers are hot. Daily temperature ranges are considerable during both the winter and summer months. Although precipitation is highly variable, it averages about 3 inches (76 millimetres) per year. Most precipitation falls from December through March. Another maximum occurs in August, characterized by thunderstorms. These storms can cause tremendous flash floods that rush into areas where no precipitation has fallen. Little precipitation falls in May and June. Snowfall occurs occasionally over the northern plateaus. Another feature of the dry subtropics are the hot, southerly winds that often carry dust from the interior. Although they occur at various times of the year, they are especially common during the spring. In Egypt they are known as the khamsin, in Libya as the ghibli, and in Tunisia as the chili. The dust-laden haboob winds of Sudan are of shorter duration, chiefly occur during the summer months, and often usher in heavy rains.

The dry tropical climate to the south is dominated by the same high-pressure cells, but it is regularly influenced by the seasonal interaction of a stable continental subtropical air mass and a southerly, unstable maritime tropical air mass. The annual range in average daily temperatures in the dry tropical regions of the Sahara is approximately 31.5 °F (17.5 °C). Average temperatures for the coldest months are essentially the same as they are for the subtropical zone to the north, but the diurnal range is more moderate. In the higher elevations of the zone, the lows approximate those of more northerly, subtropical regions. For example, absolute lows of 5 °F (−15 °C) have been recorded in the Tibesti Mountains. Late spring and early summer are hot; high temperatures of 122 °F (50 °C) are not unusual. Although the massifs of the dry tropics often receive small quantities of precipitation throughout the year, the lowlands have a single summer maximum. As in the north, much of this rainfall occurs as thunderstorms. Precipitation averages are about five inches per year, occasionally including some snowfall in the central massifs. In the western margin of the desert the cold Canary Current reduces air temperatures, thereby reducing convectional rainfall, but resulting in higher humidity and occasional fogs. In the southern Sahara the winter is the period of the harmattan, a dry northeasterly wind laden with sand and other easily transported dust particles.