© 2019 Wiley Periodicals, Inc. In this work, we study the position and momentum information entropies of multiple quantum well systems in fractional Schrödinger equations, which, to the best of our knowledge, have not so far been studied. Through a confining potential, their shape and number of wells (NOW) can be controlled by using a few tuning parameters; we present some interesting quantum effects that only appear in the fractional Schrödinger equation systems. One of the parameters denoted by the Ld can affect the position and momentum probability densities if the system is fractional (1 < α < 2). We find that the position (momentum) probability density tends to be more severely localized (delocalized) in more fractional systems (ie, in smaller values of α). Affecting the Ld on the position and momentum probability densities is a quantum effect that only appears in the fractional Schrödinger equations. Finally, we show that the Beckner Bialynicki-Birula-Mycieslki (BBM) inequality in the fractional Schrödinger equation is still satisfied by changing the confining potential amplitude Vconf, the NOW, the fractional parameter α, and the confining potential parameter Ld.