This paper presents the quantification of uncertainties in the prediction of settlements of embankments built on prefabricated vertical drains (PVDs) improved soft soil deposits based on data collected from two well-documented projects, located in Karakore, Ethiopia, and Ballina, Australia. For this purpose, settlement prediction biases and settlement distributions were statistically computed based on analyses conducted on two Class A and Class C numerical predictions made using PLAXIS 2D finite element modelling. From the results of prediction bias, Class C predictions agreed well with the field measured settlements at both sites. In Class C predictions, the computed settlements were biased to the measured values. For Class A predictions, the calculated settlement values were in the range of mean and mean minus 3SD (standard deviations) for Karakore clay, and they were within mean and mean minus 2SD limit for the Ballina soil. The contributing factors to the settlement uncertainties of the Karakore site may include variability within the soil profile of the alluvial deposit, particularly the presence of interbedded granular layer within the soft layers, and the high embankment fills, and the limited number of samples available for laboratory testing. At the Ballina test embankment site, the uncertainties may have been associated with the presence of transitional layers at the bottom of estuarine clay and sensitivity of soft soil to sample disturbances and limitations in representing all the site conditions.