The concept of uncertainty in an isotopic analysis is not uniform in the scientific community worldwide and can compromise the risk of false compliance assessment applied to carbon isotopic analyses in natural gas exploratory evaluation. In this work, we demonstrated a way to calculate one of the main sources of this uncertainty, which is underestimated in most studies focusing on gas analysis: the δ13C calculation itself is primarily based on the raw analytical data. The carbon isotopic composition of methane, ethane, propane, and CO2 was measured. After a detailed mathematical treatment, the corresponding expanded uncertainties for each analyte were calculated. Next, for the systematic isotopic characterization of the two gas standards, we calculated the standard uncertainty, intermediary precision, combined standard uncertainty, and finally, the expanded uncertainty for methane, ethane, propane, and CO2. We have found an expanded uncertainty value of 1.8‰ for all compounds, except for propane, where a value of 1.6‰ was obtained. The expanded uncertainty values calculated with the approach shown in this study reveal that the error arising from the application of delta calculation algorithms cannot be neglected, and the obtained values are higher than 0.5‰, usually considered as the accepted uncertainty associated with the GC-IRMS analyses. Finally, based on the use of uncertainty information to evaluate the risk of false compliance, the lower and upper acceptance limits for the carbon isotopic analysis of methane in natural gas are calculated, considering the exploratory limits between −55‰ and −50‰: (i) for the underestimated current uncertainty of 0.5‰, the lower and upper acceptance limits, respectively, are −54.6‰ and −50.4‰; and (ii) for the proposed realistic uncertainty of 1.8‰, the lower and upper acceptance limits would be more restrictive; i.e., −53.5‰ and −51.5‰, respectively.