[4] He previously held the positions of Secretary General for Human Rights, Coexistence and Cooperation of the Basque Government (from 2017 to 2020), General Secretary for Peace and Coexistence of the Basque Government (from 2013 to 2017) and Councillor of the City Hall of Tolosa between 1987 and 1991.

[6][8] In December 1992 he founded Elkarri, a social movement that actively worked for non-violence, human rights, dialogue, pluralism and peace in the Basque Country.

[10][11][12] After the disappearance of Elkarri, Jonan Fernández created Baketik, a foundation dedicated to promoting processes of personal, educational, coexistence, organizational or social transformation with an ethical sense.

[18] During the COVID-19 pandemic, Fernández was at the head of the advisory committee that established the health measures that should be implemented in the Basque Country.

[19][20][21][22][23] In 2021 was appointed Secretary General for Social Transition and Agenda 2030 of the Basque Government by Iñigo Urkullu, position he currently helds.