A pulse oximeter model linking arterial (SaO2) and peripheral (SpO2) oxygen saturation is the terminal part of a mathematical model of neonatal oxygen transport. Previous studies have confirmed the overestimation of oxygen saturation measured by pulse oximetry in neonates compared to arterial oxygen saturation and the large variability of measured values over time caused by measurement inaccuracies. This work aimed to determine the SpO2 measurement noise that affects the biased SpO2 value at each time point and integrate the noise description with the systematic bias between SaO2 and SpO2. The SaO2–SpO2 bias was based on previously published clinical data from pathological patients younger than 60 days requiring ventilatory support. The statistical properties of the random SpO2 measurement noise were estimated from the SpO2 continuous recordings of 21 pathological and 21 physiological neonates. The result of the work is a comprehensive characterization of the properties of a pulse oximeter model describing the transfer of the input SaO2 value to the output SpO2 value, including the bias and noise typical for the bedside monitoring of neonates. These results will help to improve a computer model of neonatal oxygen transport.