Alexandria on Monday morning saw thunder and heavy rain which disrupted traffic, Al-Ahram's Arabic news website reported. Cairo also reported rain and thunder.
Much of the rest of the country will also face unseasonal rain on Monday, as well as hot temperatures and light, dusty winds, the Egyptian Meteorological Authority has said.
Late spring is traditionally known in Egypt as khamaseen season, notorious for hot, dry sandstorms. Rain is not common.
The north coast, Sinai, the Delta region and differents parts of Cairo will all see rain on Monday, along with dusty, sandy wind in most parts of Egypt.
The northernmost parts of Upper Egypt will witness heavy winds that build to a storm.
Waves in both the Red Sea and the Mediterranean will be moderate, rising from 1 to 2 metres.
Temperatures are forecast to reach a low of 19 degrees Celsius and a high of 32 degrees in Cairo, and a low of 17 degrees and a high of 27 degrees in Alexandria.