Weather in Jerusalem in September 2016. Check the weather in Jerusalem in September before you book your next holiday in Israel. Long-term weather averages give the best indication of the weather in September 2016 and include figures for temperature, sunshine and rainfall for Jerusalem, Israel. Weather in Jerusalem in September. The average maximum daytime temperature in Jerusalem in September is a warm 29°C (84°F) with moderate heat & humidity. There are usually 11 hours of bright sunshine each day, which represents 86% of the 12 hours of daylight.