Rubinstein was born in Jerusalem in 1937. He grew up in Neveh Bezalel, a small neighborhood between Nahlaot and the city center. He majored in Middle Eastern studies and sociology at the Hebrew University of Jerusalem.
In 1967, during the Six-Day War, Rubinstein was a reserve soldier in a Jerusalem reconnaissance unit led by Yossi Langotsky. This unit was the first to cross the cease-fire line into the Jordanian-controlled West Bank.
From 1967 to 1990, Rubinstein worked as a columnist and Jerusalem bureau chief for the now-defunct newspaper Davar. From 1990-2008, he worked for Haaretz, where he was a member of the editorial board. He wrote regular columns on the Arab-Israeli conflict and Palestinian affairs. He now writes a weekly column on the Palestinian economy for Calcalist, an Israeli business daily published by Yediot Ahronoth.
In 2007, Rubinstein described Israel as an "apartheid state" at the UN-sponsored International Conference of Civil Society in Support of Israeli-Palestinian Peace. In response, the Zionist Federation of Great Britain cancelled his scheduled appearance at an event sponsored by the Federation. Its chairman, Andrew Balcombe said: "Criticism of Israeli policy is acceptable. However, by using the word 'apartheid' in a UN conference held at the European Parliament, Danny Rubinstein encourages the demonization of Israel and the Jewish people." At an event sponsored by the New Israel Fund, Rubinstein was not apologetic: "People do use the word 'apartheid' in my circles. My newspaper increasingly uses that word. This is nothing new."
- Camp David 2000 (2002)
- The Mystery of Arafat (1995) 
- People of Nowhere (1991)
- Silverstein, Richard (6 September 2007). "Don't mention the A-word". The Guardian. Retrieved 12 September 2011.
- A walk across Jerusalem history - Haaretz - Israel News
- Jewish Women's Archive
- A palace befiting the ruler of the land - Haaretz - Israel News
- Keeping the Two State Solution Alive
- Lappin, Yaakov (31 August 2007). "Zionist Federation cancels Haaretz journalist". Ynetnews.com. Retrieved 26 September 2011.
- Spritzer, Dinah A. "Israeli journalist dares to use dreaded A word". Jewish Review. Retrieved 26 September 2011.
- Amazon.com: The Mystery of Arafat: Danny Rubinstein, Dan Leon: Books