In the second half of the 1990s and early 2000s, some sub-Saharan African countries have experienced a levelling off of their fertility decline and in some cases even a reversal leading to an increase–so-called stalling in the fertility transition. Goujon, Lutz and KC postulated in 2015 that the structural adjustment programs (SAPs) may have resulted into education discontinuities, due to budget cuts in the social sector, which may in turn have been causing the stalls in fertility. We explore the link further by using longitudinal cohort-educational trends and longitudinal cohort-age specific fertility trends from retrospectively collected consecutive demographic and health surveys (DHSs) conducted in the region. By applying the tools of panel data econometrics techniques to DHSs, we provide micro-level evidences that the educational discontinuities experienced during the implementation period of SAPs partially, but not fully, explain the stalling in the fertility transition experienced in the region.