Previous epidemiological studies on health effects of radiation exposure from mobile phones have produced inconsistent results. This may be due to experimental difficulties and various sources of uncertainty, such as statistical variability, measurement errors, and model uncertainty. An analytical technique known as the Monte Carlo simulation provides an additional approach to analysis by addressing uncertainty in model inputs using error probability distributions, rather than point-source data. The aim of this investigation was to demonstrate using Monte Carlo simulation of data from the ExPOSURE (Examination of Psychological Outcomes in Students using Radiofrequency dEvices) study to quantify uncertainty in the output of the model. Data were collected twice, approximately one year apart (between 2011 and 2013) for 412 primary school participants in Australia. Monte Carlo simulation was used to estimate output uncertainty in the model due to uncertainties in the call exposure data. Multiple linear regression models evaluated associations between mobile phone calls with cognitive function and found weak evidence of an association. Similar to previous longitudinal analysis, associations were found for the Go/No Go and Groton maze learning tasks, and a Stroop time ratio. However, with the introduction of uncertainty analysis, the results were closer to the null hypothesis.