Metabolomic analysis of bronchoalveolar lavage fluid (BALF) may help understand the pathophysiology of pulmonary diseases such as asthma. However, a major analytical challenge is that most metabolites in BALF are in low abundance and further diluted by the collection procedure. Here we report a sensitive metabolomic profiling method based on 12C-/13C-differential isotope dansylation that targets amine- and phenol-containing metabolites, solid phase extraction for analyte enrichment, and liquid chromatography Fourier transform ion cyclotron resonance-mass spectrometry (LC–FTICR-MS). This method detected 250 ion pairs or putative metabolites in rat BALF and 36 of them were positively identified. The majority were not reported in previous studies using NMR or conventional LC–MS. The developed isotope labeling method was then applied to investigate metabolomic changes in BALF samples from a model of allergic asthma in rats. Statistical analysis of the resultant data showed that there was distinct separation between normal and inflamed rats. Metabolic pathway analysis indicated that the arginine-proline metabolic pathway was dysregulated in rats with experimental asthma.