Ionospheric irregularities of the E–F valley region are relatively less explored with in situ experiments enabling to capture local fine structures. Here, we present the multifractal analysis of electron density fluctuations in the E–F valley region, obtained from a rocket experiment performed at equatorial low latitude station, Alcântara, Brazil to explore scaling structures in the plasma irregularities. The multifractal spectrum is validated with a analytical model that mimics the energy distribution in a turbulent cascade using probabilistic weights. We report the nature of the E–F valley region irregularities to be multifractal, asymmetric, intermittent and non–homogeneous. The multifractal measures show transition of the influence from smaller to larger fluctuations as the rocket approaches the F layer base, consolidating earlier observations. By identifying the nature of the irregularities, we explore the possible cause for a wide variation reported in the spectral indices. Our analysis demonstrates the usability of the multifractal approach in studying the nonlinear fluctuations observed from the E-F valley region in situ data.