The aim of this study was to identify chemicals migrating from paper-based food packaging materials by GC-Orbitrap mass spectrometry (MS). Migration tests were conducted with samples of butcher paper, liquid egg containers, pizza boxes and pizza box liners. A new approach for an automated data processing of GC-Orbitrap EI data was developed and evaluated with Compound Discoverer™ software. A total of 35 migrated chemicals were putatively identified. They represented natural compounds, fatty acid ethyl esters, FDA substances added to food and Indirect Additives in Food Contact Substances, common phthalates, alkanes, siloxanes, ketones, and chemicals used as additives in packaging. Additionally, some unexpected compounds suspected to be degradation products of additives were identified. Levels of 23 identified chemicals significantly (p < 0.05) changed over the 10-day migration test. For two identified migrants, dibutyl phthalate and benzophenone, calculated specific migration limits (SMLs) were below the established regulatory levels. The information on the identity of chemicals migrating from food packaging materials is important to inform regulatory agencies and to develop risk management strategies.