The day‐to‐day variations (or the weather) of an additional layer, called the F3 layer, that has been predicted to exist at altitudes above the F2 peak in the equatorial ionosphere are studied through ionosonde observations and theoretical modeling. The ionograms recorded in 1995 at the equatorial station Fortaleza (4°S, 38°W; dip angle 9°S) in Brazil show the occurrence of the F3 layer during daytime from 0800 to 1630 LT, with the duration of occurrence ranging from 15 min to 6 hours. Although the layer occurs most frequently (75% of the days) in local summer as previously predicted, there are consecutive and individual magnetically quiet and disturbed days when the layer does not occur. There are also days when the layer reoccurs. The model results, obtained using the Sheffield University plasmasphere‐ionosphere model, show that the day‐to‐day variations of the F3 layer arise from the corresponding variations of the vertical plasma velocity. The layer occurs when the time‐cumulative vertical velocity displaces the daytime F2 peak to high altitudes, to form the F3 layer, while the normal F2 layer develops at low altitudes. Sudden displacements result in more distinct F3 layers than gradual displacements. Model results also show that the plasma temperature within the F3 layer decreases as the plasma density increases, and, like the plasma density, the plasma temperature also undergoes large day‐to‐day variations.