The urine levels of organophosphate flame retardants (PFRs) and bisphenol A (BPA) in kindergarten children (n = 31, 4–6 years old, sampling performed in 2016) in Hong Kong were measured. The detection frequency of the target PFRs, tri(2-chloroethyl)phosphate (TCEP), tris(1,3-dichloro-2-propyl) phosphate (TDCIPP), tris(chloroisopropyl)phosphate (TCIPP), triphenyl phosphate (TPHP) and 2-ethylhexyl diphenyl phosphate (EHDPP) ranged from 52% to 84%. The 95th percentile urinary concentrations of TPHP, TDCIPP, TCIPP, EHDPP and TCEP were 1.70, 0.24, 0.03, 0.05, 0.68 and 0.03 ng/mL, respectively. The median urine level of BPA was 1.69 ng/mL, with a detection frequency of 77%. Due to the lack of metabolism information, two scenarios were used to calculate the estimated daily intake (EDI) of these compounds. Back-calculated EDIs of PFRs using the urinary excretion rates from in vivo animal data (scenario 2) were up to 2.97 μg/kg/d (TDCIPP), which was only a little less than that observed in a sample of American infants, and the reference dose (RfD), meaning that the potential health risk of TDCIPP cannot be ignored. Dust ingestion was suggested to be the major pathway of exposure to PFRs, but when the levels in dust and air particles in kindergartens in Hong Kong were used to predict EDIs, these values were nearly half as much as those predicted from urinary TDCIPP in this study. This suggested that children's PFRs burden may be underestimated when considering only PFR levels in dust or air. There is thus a need for further studies with large-scale surveys and investigation of exposure routes.