In March 2021, after having been held without charge since 2019, she was sentenced by an Israeli military court to two years in prison after a plea bargain, in which she declared herself guilty of membership in an organization, the PFLP, which Israel regards as a terrorist group.

[9] She has gone on record to state that her plea bargaining is due to the exhaustingly protracted nature of legal proceedings, lack of faith in Israel's military courts, and the threat, unless she admits guilt, of serving a 7-year sentence.

[14] In 1985, after a five-year engagement, and when she had completed her master's degree at Bir Zeit,[15] Jarrar married Ghassan Jarrar, a fellow student, and now a manufacturer of children's furniture and toys at Beit Furik,[16][17] a former political activist who has been arrested 14 times and spent 10–11 years without trial or charges being laid under administrative detention in Israeli prisons.

[19][20][21] In her six years of imprisonment, she has been refused leave to attend her father's funeral (2015), that of her mother (2018), of her daughter Suha (2021) who died aged 31.

On Suha's death from cardiac arrest in July 2021, Jarrar was denied a temporary release from her imprisonment on humanitarian grounds in order to attend her daughter's funeral.

[3] Since 1998 Jarrar has been banned from traveling outside of the occupied Palestinian territories, after she attended the Human Rights Defenders' Summit in Paris that year.

[24] Since March 2006, she has been the PFLP's senior political leader, after the group's Secretary General Ahmad Sa'adat was arrested and placed in solitary confinement.

[23] Jarrar has suffered from bouts of deep vein thrombosis, and her lawyer has expressed concern that appropriate medical care for her condition might not be available in an Israeli prison.

[25] In July 2010, Jarrar was informed by a doctor that tests indicated she needed an urgent brain scan to establish an exact neurological diagnosis.

Since the medical equipment to make the diagnosis was not available in the West Bank, where she was then detained, she was informed that the PNA's Health Ministry would cover the costs of her hospitalization in Amman, but not in Israel.

On August 29, she was denied transit to Jordan via the Allenby Bridge, and Shin Bet stated that she was a security threat to the region.

[27][28] On 20 August 2014, approximately 50 Israeli soldiers surrounded Jarrar's home in Ramallah, and an Israeli officer gave her an expulsion order stating she was a threat to the security of the region and was to leave her home of residence, Ramallah, and transfer to the district of Jericho where she was to live under a restricted movement protocol for six months.

[20] A six-month administrative detention, which can be renewed indefinitely,[29] was issued against her by Central Command Chief Gen. Roni Numa and was reviewed by a military court on April 8,[7] where it was confirmed, despite international protests.

[28] Amnesty International noted that Jarrar suffers from chronic health problems, with the prospect of facing indefinite detention without charge or trial.

[35] 58 Members of the European Parliament protested her arrest in an open letter to Federica Mogherini, stating that attempts to forcibly transfer a person under occupation, to which she was subject in August 2014, constituted a violation of the Fourth Geneva Convention.

[6] Haaretz stated at the time of her arrest: 'If Jarrar broke the law, Israel must put her on trial and prove she committed a crime.

'[32]Her administrative detention led to formal imprisonment pending a trial, which began with a closed session on April 15, at a military criminal court at Ofer Prison where the prosecutor at the Israeli military court laid 12 charges against her, based on her association with the PFLP, including membership of an organization Israel classifies as illegal; participation in protests, and incitement to kidnap Israeli soldiers.

[4] Several counts refer to her having given interviews, speeches and lectures, participating in marches and a politicized book fair, calling for Palestinian prisoners to be released, and opposing the Israeli occupation.

[15] The indictment also spoke of suspicions she had visited the homes of prisoners’ families, and of having attended a book fair, of calling for the release of Ahmad Saadat, a leader of the Popular Front for the Liberation of Palestine.

[36] On April 26, a Haaretz editorial argued that the Military Advocate General had decided to press terrorist charges against her only after her arbitrary detention aroused international criticism and that a suspicion exists was that the trial was payback for her involvement in Palestine's successful entry into the ICC.

In early August,[54][55][56] without informing her family, and still requiring medication, she was incarcerated in a windowless cell measuring 2.5 x 1.5 meters at Neve Tirza and was kept in solitary confinement.