Volatile organic compounds (VOCs) in urine headspace are potential biomarkers for different medical conditions, as canines can detect human diseases simply by smelling VOCs. Because dogs can detect disease-specific VOCs, gas chromatography–mass spectrometry (GC–MS) systems may be able to differentiate medical conditions with enhanced accuracy and precision, given they have unprecedented efficiency in separating, quantifying, and identifying VOCs in urine. Advancements in instrumentation have permitted the development of portable GC–MS systems that analyze VOCs at the point of care, but these are designed for environmental monitoring, emergency response, and manufacturing/processing. The purpose of this study is to repurpose the HAPSITE^® ER portable GC–MS for identifying urinary VOC biomarkers. Method development focused on optimizing sample preparation, off-column conditions, and instrumental parameters that may affect performance. Once standardized, the method was used to analyze a urine standard (n = 10) to characterize intra-day reproducibility. To characterize inter-day performance, n = 3 samples each from three volunteers (and the standard) were analyzed each day for a total of four days (n = 48 samples). Results showed the method could detect VOC signals with adequate reproducibility and distinguish VOC profiles from different volunteers with 100% accuracy.