The concert was given in memory of Edward Said, the Palestinian-American scholar and co-founder of the orchestra, who died in 2003.
Said and Barenboim, who was raised in Israel, founded the orchestra in 1999.
The concert, a program of works by Beethoven and Mozart, was performed before a standing-room-only crowd in the 700-seat Ramallah concert hall. Those who could not fit in the hall watched the concert on closed-circuit television in a hallway outside.
Barenboim himself has performed before in Ramallah, but it is the first time for his orchestra, which has musicians from Israel, the Palestinian territories, Syria, Lebanon, Egypt, and Jordan. A concert scheduled for last year had to be canceled for security reasons.