Evaluating the safety of e-cigarettes and making informed judgement about developing potential standards require sufficient scientific evidence. Since e-cigarettes are highly engineered products containing plastic, glass and metal parts, and e-liquids are largely different matrices, many toxic compounds which are not typical hazards for the users of combustible tobacco products (e.g., cigarettes), could exist in e-liquids, and consequently, posing potential health risk to e-cigarette users. We combined the measurements of urinary metabolites of organophosphate flame retardants (OPFRs) with questionnaire data collected in the National Health and Nutrition Examination Surveys (NHANES) from 2013 to 2014, and we compared adjusted geometric means (GM) for each biomarker in e-cigarette users with levels in non-users and users of various tobacco products using multiple regression analyses to adjust for potential confounders. We found diphenyl phosphate (DPhP), bis(1,3-dichloro-2-propyl) phosphate (BDCPP), bis(2-chloroethyl) phosphate (BCEP), and dibutyl phosphate (DBUP) were detected in all e-cigarette users. The adjusted GM of BCEP, the metabolite of tris(2-chloroethyl) phosphate (TCEP), was 81% higher than nonusers (p = 0.0124) and significantly higher than those for both cigarette and cigar users (p < 0.05). The findings in this pilot study suggest that certain OPFRs may present in e-cigarettes as contaminants, and consequently, resulting in higher exposure levels in e-cigarette users compared to nonusers. As we only identified 14 e-cigarette users in the survey, the findings in this study need to be confirmed in future study at a larger scale. A better examination of the types and levels of FRs and their potential contamination sources in e-cigarettes is also needed.