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
- "Danny Rubinstein | Jewish Women's Archive". jwa.org. Retrieved 2019-06-05.
- 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.
- "The Mystery of Arafat". www.amazon.com. Retrieved 2019-06-05.