Pyrrolizidine alkaloids (PAs) are secondary metabolites produced by plants as a chemical defense against herbivores. Plants containing PAs are widely distributed in almost all geographical regions posing a risk of honey contamination. To provide safety of honey and decrease the potential risk for the consumers, a sensitive method based on gas chromatography-mass spectrometry enabling determination of a content of 1,2-unsaturated PAs in honey was developed. Honey samples were purified on MCX cartridges, and PAs were eluted with a solvent mixture consisting of ethyl acetate, methanol, ammonia, and triethylamine. Subsequently, 1,2-unsaturated alkaloids were reduced to their common backbone structures and derivatized with heptafluorobutyric anhydride. The method was validated according to SANTE 2015. All received parameters are in consistence with the document requirements as recovery ranged from 73.1 to 93.6%. The repeatability and reproducibility were calculated as relative standard deviation and ranged from 3.9 to 8.6% and from 10.6 to 17.8%, respectively. The limit of quantification was determined as 1 μg kg−1. Good linearity of the method was obtained with the coefficient of determination R2 > 0.99. The method was applied to 40 Polish and 14 Asian honey sample analyses.