In recent years, the production and usage volumes of organophosphate flame retardants (OPFRs) has increased substantially. Certain OPFRs are suspected reproductive toxins, carcinogenic, and neurotoxic. Insufficient information is available on human exposure pathways to these chemicals, particularly in Australia. We aim to assess the association between OPFR concentrations in the urine of children to environmental and behavioural risk factors. Concentrations of eight OPFRs and eleven metabolites were measured in the urine of 51 children, aged 3–29 months, in Southeast Queensland, Australia and compared to their behavioural and environmental risk factor data obtained by an online questionnaire. Of the 11 OPFR metabolites analysed, 55% were frequently detected in the majority (> 80%) of samples. The most frequently detected metabolite was bis(1,3-dichloroisopropyl) phosphate (BDCIPP) (detected in 100% of samples), followed by 1-hydroxy-2-propyl bis(1-chloro-2-propyl) phosphate (BCIPHIPP) (96%), diphenyl phosphate (DPHP) (94%) and bis(1-chloroisopropyl) phosphate (BCIPP) (86%). In multivariable modelling, age was positively associated with concentrations of bis(2-butoxyethyl) phosphate (BBOEP) and negatively associated with concentrations of BCIPP and BCIPHIPP. Other non-age related factors, including vacuuming frequency, hand-washing frequency and presence and number of some electrical appliances in the home were also associated with concentrations of OPFR metabolites.