Information about the altitudinal distribution of ionospheric electron density (Ne) in the African equatorial region is very scanty. Such information is vital in modeling of key ionospheric parameters and in solving problems associated with ionospheric effect on the applications that depend on space-based positioning and navigation systems. For the first time in the region, the entire Ne profile estimated by IRI is evaluated with profile deduced from Digisonde measurements at Ilorin (geog. 8.50°N, 4.50°E; dip. −7.9°) during low solar activity condition. Results obtained indicate marked discrepancies between the two profiles with magnitudes revealing local time and altitudinal and seasonal trends. The largest discrepancies are found between the post-sunset and sunrise hours regardless of the seasons. IRI underestimates the Ne around the F1 region and is most obvious in September equinox and December solstice with deviation up to −42%. Further, IRI overestimates the Ne around the F2 peak at daytime, mostly in solstices with maximum deviation of 26% at F2 peak. All the three IRI topside models generally underestimate Ne between ~F2 peak height and ~800 km in all seasons except in June solstice. Beyond 800 km, the Digisonde, IRI-NeQuick, and IRI-2001 Corr profiles tend to converge, whereas the IRI-2001 profiles still show marked divergence from the Digisonde profile in all seasons. Overall, the IRI-NeQuick gives the best topside representation at this station at daytime/nighttime. The comparative analysis of Digisonde-TEC and GPS-TEC suggests that the Digisonde alone may not give a reliable estimate of the nighttime topside altitudinal distribution of Ne at this location.