Distinguishing chemicals and improvement on analytical methods has a direct impact on modern chemical analysis. In this work, the dissociative ionization of xylene isomers was investigated using a femtosecond laser mass spectrometry (FLMS) method with a custom-built linear time-of-flight (TOF) instrument. Laser beams at 800 nm and 400 nm were used and intensity-dependent analysis of the obtained mass spectra was performed using principal component analysis (PCA) to distinguish the xylene isomers, which give identical mass spectra in appearance that cannot be distinguished using normal mass spectrometry methods. The results show that there is a statistically highly significant difference between the xylene isomers for two principal components (1 − α > 99.99%) and minimal information loss (<5%) took place during the PCA procedure. Also, the use of the k-medoid clustering method showed that the isomers may be distinguished in real-time for a wide range of ionization laser pulse powers with approximately 99% accuracy. The results suggest that real-time isomer analysis by the FLMS method is suitable for mass spectral identification applications. The FLMS method has been shown to be an important alternative to other mass spectrometric methods that use different ionization mechanisms.