He was born in Budapest, Hungary. After the Second World War, Jalics left his motherland and went to Germany to become a part in the Jesuit order. He studied philosophy in Belgium. In the late 1950s he lectured in Chile and Argentina on dogmatic theology.
While doing social work in 1976 during the Dirty War in a poor neighborhood, Jalics and Orlando Yorio were captured by a death squad, abducted, and held captive for five months. Father General Pedro Arrupe in Rome was informed by letter during the abduction. Both Jalics and Orlando Yorio left the Jesuit Order, but were later offered reinstatement to it: Jalics accepted but Yorio did not.
On 15 April 2005, a human rights lawyer filed a criminal complaint against Cardinal Jorge Mario Bergoglio, S.J.—then the Archbishop of Buenos Aires (and became Pope Francis in 2013)—as superior in the Society of Jesus of Argentina, accusing him of involvement in the kidnapping.
On 15 March 2013, Fr. Jalics made a public statement on the occasion of the election of his former superior, who as Pope had taken the same name (Ferenc is Hungarian for Francis), describing how they met up again years later and had concelebrated Mass together: „Ich bin mit den Geschehnissen versöhnt und betrachte sie meinerseits als abgeschlossen.“ (I have been reconciled to the events and from my side consider them closed") Fr. Jalics wished God's providential blessing on the Pope: "Ich wünsche Papst Franziskus Gottes reichen Segen für sein Amt. (signed) P. Franz Jalics SJ, 15. März 2013" ("I hope God will bless Pope Francis abundantly in his duties") Fr. Jalics subsequently elaborated on his experiences, in particular how a female lay catechist was culpable for their denunciations, "Wie ich in meiner früheren Erklärung deutlich gemacht habe, sind wir wegen einer Katechetin verhaftet worden, die zuerst mit uns zusammenarbeitete und später in die Guerilla eintrat [aufgrund eines Übersetzungsfehlers wurde sie in der vorigen Erklärung als Mann bezeichnet]." (As I made perfectly clear in my prior statement, we were arrested because of a female catechist, who had at first collaborated with us and then later joined the guerillas [whose identity, owing to a translation error, was characterized as male in the earlier statement]). The second public statement was issued a week later, March 20, 2013, also through the Jesuits' German Province.
- Miteinander im Glauben wachsen: Anleitung zum geistlichen Begleitgespräch. Aus dem Spanischen von Isabella Jalics, Würzburg: Echter, 2008, ISBN 978-3-429-02988-3.
- Contemplative retreat. An introduction to the contemplative way to life and to the Jesus prayer (translated by Lucia Wiedenhöver), Longwood: Xulon Press, 2003, ISBN 1-594671-56-7.
- The contemplative way. Quietly savoring God's presence (translated by Matthias Altrichter), New York: Paulist Press, 2011, ISBN 978-0-809-14722-9.
- Die geistliche Begleitung im Evangelium, Würzburg: Echter, 2012, ISBN 978-3-429-03482-5.
- Horacio Verbitsky: Los signos del cardenal. In: Página/12, 2. Mai 2010. Accessed 1 January 2011.
- "Argentine Cardinal Named in Kidnap Lawsuit". Los Angeles Times. Associated Press. 17 April 2005. Retrieved 2013-03-13.
- "Jesuit Jalics nimmt Stellung zu den Vorwürfen gegen den neuen Papst" KATH.NET German language religious news site, Linz, 15 März 2013, (Retrieved March 15, 2013)
- "Jesuiten-Pater aus Oberfranken Junta-Opfer Jalics mit Papst versöhnt" Online news article posted at Bayerischer Rundfunk (Bavarian Public Television) Stand: 15.03.2013
- Public Position Statement published by German Province of Jesuits
- Pope Francis did not denounce me to Argentinian junta "says priest Francisco Jalics, who was imprisoned for five months in the 1970s, says he and the new pope reconciled in 2000" Jonathan Watts, Guardian, UK newspaper, March 21, 2013
- "Second Declaration of Father Franz Jalics SJ" (in German). German Jesuit Web site. 20 March 2013.