The itinerary I suggest includes full days, though of course you can choose to see less or more. If you have limited time, don’t try to cram everything into one day. Focus on the sites that are most important to you.
Day 1 – Mount of Olives and the Old City
I suggest starting the day from the Mount of Olives, because it is the highest point in Jerusalem. From there on, your trip will be downhill and the sun at your back. (You can reach it on foot, through the Lions’ Gate and then ascending the Mount of Olives, or by taxi. There’s no good public transportation to the Mount of Olives from the city center.) Keep in mind though that most tour groups start from the Mount of Olives, and therefore, during high season, mornings are very crowded on the Mount of Olives.
If you want to visit the Temple Mount in the Old City, it’s highly recommended. Pay attention to the opening hours. If you still have energy left, you can also visit Mount Zion, but you can leave this visit for another day.
*Can be combined with a visit to the Western Wall Tunnel (advance registration required) or the City of David.
*Lunch can be eaten in the Old City.
*Sandemans tours, which depart from Jaffa Gate, are a good way to get a first impression of the city. Most of their guides are good. I used to be one of them.
*On this day, you will spend a lot of time outdoors. If it is expected to a particularly hot or cold day, it might be a good idea to start instead with the day dedicated to museums (Day 2 on the itinerary) – Yad Vashem and the Israel Museum, for example.
Jewish sights which can be integrated into this day – Hurva Synagogue, Rambam Synagogue, and the Four Sephardic Synagogues.
Protestant sights which can be integrated into this day – Augusta Victoria on the Mount of Olives, Church of the Redeemer in the Old City, and the Garden Tomb (a few minutes’ walk from Damascus Gate). Note that most of Jerusalem’s churches belong to the Catholic and Orthodox denominations, which came earlier.
Day 2 – Knesset (Israeli Parliament) and Israel Museum
You can start the day with a tour of the Knesset (on Sundays and Thursdays, there are free tours in different languages; advance registration at the Knesset is required). The Israel Museum is close by and is definitely worth a visit – it has the most impressive displays in Israel. After visiting the museum, you can return to the city center to visit and grab something to eat at the Mahane Yehuda Market.
Day 3 – Ein Karem, Mount Herzl, and Yad Vashem
Mount Herzl contains a number of important sites to help understand Israeliness. Theodore Herzl and former prime ministers and presidents of the state are buried at the top of the mountain. Down the slopes of the mountain is Israel’s largest military cemetery and Yad Vashem, which deals with the Holocaust of the Jewish people. From Yad Vashem, you can head either on foot or by bus from the light rail station to Ein Karem – a quiet village at the outskirts of the city. There are two important churches in this neighborhood, the Church of the Visitation and the Church of St. John the Baptist. There are also many small and pleasant places where you can sit back and relax after the hustle and bustle of Jerusalem.
More sights in Jerusalem:
Gethsemane – the hardest point in Jesus’ life
The Mount of Olives – the place to be at the end of days…
The Chapel of the Ascension – a mosque that turns into a church…
The Church of the Holy Sepulchre
The Wailing Wall (Kotel) – not the holiest place for the Jews.
The Old City of Jerusalem – the holiest square kilometer in the world
The most important museums in Jerusalem