The effect of different heat treatments of camelina (Camelina sativa) seeds on the phenolic profile and antioxidant activity of their hydrolyzed extracts was investigated. The results showed that total phenol contents increased in thermally treated seeds. Heat treatment affected also the quantities of individual phenolic compounds in extracts. Phenolics in unheated camelina seeds existed in bound rather than in free form. A temperature of 160 °C was required for release of insoluble bound phenolics, whereas lower temperatures were found to be optimal to liberate those present as soluble conjugates. The best reducing power and alkyl peroxyl radical scavenging activity in the emulsion was expressed by phenolics which were bound to the cell wall, whereas the best iron chelators and 2,2-diphenyl-1-picrylhydrazyl (DPPH•) radical scavengers were found to be those present in free form. The heat treatment of seeds up to 120 °C increased the reducing power and DPPH• radical scavenging ability of extracts, but negatively affected iron chelating ability and their activity in an emulsion against alkyl peroxyl radicals.