We were interested in whether the urinary proteome could indicate the impact of e-cigarettes on the body. Urine samples were taken from a rat model of e-cigarette use before, during, and after 2 weeks of smoking. The urine proteomes of each rat were compared individually before and after smoking, while a control group was established to eliminate any differences due to the rats’ growth and development. On day 3, fetuin-B, a biomarker for Chronic Obstructive Pulmonary Disease (COPD), and annexin A2, known as a marker for multiple tumors, were identified as differentially expressed proteins in five out of six smoking rats. Interestingly, we also found that odorant-binding proteins, which are produced in the olfactory epithelium, were significantly upregulated. The pathways enriched by these differential proteins included the apelin signaling pathway, folate biosynthesis pathway, arachidonic acid metabolism, and pathways related to chemical carcinogenesis involving DNA adducts and reactive oxygen species. These pathways have been linked to the immune, cardiovascular, and respiratory systems, among others. Thus, the urinary proteome appears to reflect the effects of e-cigarettes in rats.