The measurement uncertainty (MU) of methamphetamine (MA) and amphetamine (AP) was estimated in an authentic urine sample with a relatively low concentration of MA and AP using the bottom-up approach. A cause and effect diagram was deduced; the amount of MA or AP in the sample, the volume of the sample, method precision, and sample effect were considered uncertainty sources. The concentrations of MA and AP in the urine sample with their expanded uncertainties were 340.5 +/- 33.2 ng/mL and 113.4 +/- 15.4 ng/mL, respectively, which means 9.7% and 13.6% of the concentration gave an estimated expanded uncertainty, respectively. The largest uncertainty originated from sample effect and method precision in MA and AP, respectively, but the uncertainty of the volume of the sample was minimal in both. The MU needs to be determined during the method validation process to assess test reliability. Moreover, the identification of the largest and/or smallest uncertainty source can help improve experimental protocols.