Accurate measurement of sub-picosecond aperture jitter when testing state-of-the-art high-speed, high-resolution data converters is a difficult problem, since there is no systematic method of precisely separating aperture jitter from input and clock jitter components as well as additive noise. In addition, it is more difficult to implement Built-in Self-test (BIST) schemes for accurately measuring aperture jitter based on a low cost approach, since jitter-induced noise present in the Device Under Test (DUT) degrades the performance of the Design for Test (DfT) circuitry as well as the DUT. These problems result in low test accuracy and serious yield loss. This paper presents a novel methodology for accurate prediction of aperture jitter using a cost-effective loopback methodology. Aperture jitter is precisely separated from input and clock jitter as well as additive noise present in the DUT, by using an efficient loopback scheme along with spectral characteristic equations. Hardware measurement results show that this approach can be effectively used to predict the aperture jitter of a DUT, with a significant reduction in the prediction error compared with previous approaches.