The essential oil of a protected Spanish species, Thymus praecox ssp. penyalarensis, was firstly analyzed [Gas Chromatography-Mass Spectrometry (GC-MS)] from wild populations during the phenological stages of flowering and fruiting. In flowering, the yield was 1.2%, and the major components were identified as thymol (18.5%), p-cymene (14.6%), carvacrol (11.6%), and γ-terpinene (10.1%). In fruiting, the yield was 0.9% and the major components resulted to be p-cymene (19.0%), carvacrol (16.5%), and borneol (10.5%). An experimental cultivation of the taxa was made also in order to analyze its essential oil as well. The yield was 1.3%, and the main compounds were thymol (19.1%), p-cymene (17.0%), and γ-terpinene (12.3%). Finally, the composition of the essential oil of this plant is discussed in relation to chemotaxonomic and biogeographical aspects.