Pannier-Runacher was born as the daughter of a top executive at oil company Perenco. She is a graduate of HEC Paris (1995), Sciences Po and the École nationale d'administration (ENA), where her classmates included Alexis Kohler.
Pannier-Runacher joined the French Civil Service in 2000. She first worked at the Inspection générale des finances and then joined the Assistance Publique – Hôpitaux de Paris in a managerial role from 2003 to 2006. In 2006 she joined the Caisse des dépôts et consignations as deputy director in charge of strategy and finances. In 2009 she became executive director of the Strategic Investment Fund.
Pannier-Runacher joined the private company Faurecia in 2011. In 2013 she became deputy director at the Compagnie des Alpes in charge of development and performance of skiing and leisure centers.

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