The fire at the offices of B'Tselem, an Israeli group that monitors human rights among Palestinians, took place at a time of heightened tensions.
Scores of people have been killed in several months of violence in Israel and the occupied West Bank.
Firefighters arrived at the offices, in a quiet Jerusalem neighbourhood and extinguished the blaze, Reuters news agency reported.
"There were no reports of casualties," police spokeswoman Luba Samri said.
Since October, Israeli forces or armed civilians have killed at least 139 Palestinians.