Husseini attended college at the University of Baghdad and the University of Cairo, where he became friendly with Yasir Arafat, an engineering student who had started the liberation group "Fatah," in the mid-1950s. He would later become leader of the Palestinian Liberation Organization (PLO). Fatah supported the use of violent means in order to command attention for the Palestinian cause. Husseini became involved with Fatah and attended a military college in Syria. He graduated in 1967 and became an officer in the fledgling Palestine Liberation Army. Husseini set up a training camp in Lebanon and assisted with other "military activities," according to an article in the Christian Science Monitor, which "included bombings and hijackings most of the world saw as terrorism." Husseini said later that although he did not approve of the tactics, they were effective in publicizing the situation.

On June 5, 1967, Israeli forces began what was later referred to as the "Six-Day War." Israel captured the Golan Heights from Syria; the West Bank and East Jerusalem from Jordan; and the Gaza Strip form Egypt. Since then, the ownership of those areas has been in dispute. Husseini moved back to Jerusalem and was soon arrested by Israeli soldiers for having two submachine guns in his home. He was jailed for a year. Throughout the 1970s, turmoil continued in the region, with another conflict breaking out in 1973. Husseini separated himself from terrorist activities and became more involved in politics. He held public forums with influential Israelis and helped with cooperative protests in conjunction with Israeli groups. Dedicating himself to peaceful solutions, he founded the Arab Studies Society in East Jerusalem in 1979, an institute for researching Palestinian history. In 1974, the Arab Summit named the PLO as the official representative body for Palestine. It was given observer status at the United Nations. Arafat, heading the PLO, signed the Camp David peace accords with Israel in 1978.

In 1982, Israel invaded Lebanon, where Arafat and other PLO officials held offices. Husseini was arrested and jailed numerous times from 1982 to 1987 for his PLO membership and was not allowed to travel outside of the country. In December 1987, a Palestinian uprising known as the intifada began on the West Bank and Gaza Strip. This revolt against the Israeli occupation was marked with violence and demonstrations. The Israeli army retaliated by striking back hard at the rioters and locking up Palestinian leaders, including Husseini, who was accused of inciting riots. The military also closed down his Arab Studies Society, though he later reopened it in his home. During Husseini's year-long prison term, he used his time to study Hebrew and English. His release was taken as a sign that Israeli defense minister, Yitzhak Rabin, was willing to compromise in order to defuse tensions in the area. Husseini, however, redirected Rabin to the PLO. That December, Husseini was placed under house arrest, purportedly because his public speeches fueled uprisings.

During the 1991 Gulf War, the PLO supported Saddam Hussein and Iraq. After the war, the United States worked to establish peace in the region and arranged a conference in Madrid, Spain, in late October 1991. Israeli prime minister Yitzhak Shamir, however, refused to negotiate with any known PLO members, so Husseini instead acted as a consultant to the Palestinian delegates. After Rabin took over as prime minister in 1992, he expressed willingness to discuss peace with the PLO, and Husseini was called to the table. However, Husseini and two other negotiators quit the talks in 1993 over differences with Arafat. He refused to accept their resignations. Subsequently, Israel officially recognized the PLO, and it was revealed that Rabin had begun secret discussions with the PLO in Oslo, Norway. In 1993, a peace agreement was signed in Washington, D.C., that allowed Palestinian autonomy in the Gaza Strip and Jericho, a town on the West Bank. It also set up a temporary authority, the Palestinian National Authority. Arafat returned to Gaza and named Husseini the minister of Jerusalem affairs for the Palestinian National Authority.

Rabin was assassinated in 1994 by a right-wing Israeli gunman. Benjamin Netanyahu, a right-of-center Likud Party member, was his replacement. This leadership change put new strains on the peace process. Netanyahu supported Jewish settlements in the region, including the construction of two Jewish housing projects in East Jerusalem. This point of contention sparked protests and violence. Husseini was injured in June 1998 when he was hit on the head by a rock. Other disputes involved residency permits and the plans for Israel to extend Jerusalem's boundaries. In addition, relations between Husseini and Arafat seemed to have soured, though Husseini continued to support the PLO publicly. As the fighting raged on into 1998, Husseini was doubtful that peace could be achieved as long as Netanyahu was prime minster. Husseini remained committed to the idea that Palestine should join with other Middle Eastern countries such as Israel, Jordan, Lebanon, Syria, and Egypt to form a larger, regional group, like the European Union.

Husseini is married and has two sons. Some observers feel he is being pushed out of the top ranks of the PLO due to his differences with Arafat, especially on human rights issues. Other argue that he could be in line as a successor, though Husseini denies the talk. He insists that if Jerusalem is not the capital of Palestine, then he will not become its leader.