“The United States government needs to increase its pressure on its military allies in Egypt to allow Zaree and other human rights defenders to work without harassment or fear of imprisonment,” Brian Dooley, a jury member from the group Human Rights First, said in a statement.

The other finalists for the award included Karla Avelar, a transgender woman in El Salvador who survived rape and attempted murder to work on behalf of gay, lesbian, bisexual and transgender people; and a group of five Cambodian human rights defenders who spent more than a year in pretrial detention as part of a crackdown by Prime Minister Hun Sen to deter opposition ahead of an election next year.

The candidates were picked for their bravery and because the jury saw them as emblematic of the increasing hardships that human rights defenders face globally, said Phil Lynch, a jury member and director of the Geneva-based International Service for Human Rights.

Michael Khambatta, the director of the Martin Ennals Foundation, said that the circumstances in Egypt were “clearly a major factor in this award.”

The Cairo Institute moved its headquarters to Tunisia in 2014 after its founder and a member of its board of directors received death threats, leaving Mr. Zaree as country director in Egypt. The Egyptian government froze the assets of the institute and six other organizations in 2016 and then opened an investigation of Mr. Zaree on charges that carry a possible 30-year jail term.

The charges include defaming the image of Egypt, an action seen as posing a threat to national security, and cooperating with annual reviews by the United Nations’ Human Rights Council. Mr. Zaree also faced harassment and intimidation by the state-run news media, which demonized him as a traitor, foreign agent and spy, the Martin Ennals Foundation said.

As a member of the Human Rights Council, Egypt has an obligation to uphold rights and cooperate with United Nations mechanisms. But Mr. Zaree’s experience fits a wider pattern of repression in which the authorities have targeted other activists for working with the United Nations. Egyptian security agents seized Ebrahim Metwally Hegazy, a lawyer and human rights defender, at Cairo’s international airport last month as he was en route to Geneva to testify before a United Nations panel on enforced disappearances.