The internal morphology and magnetic properties of layer-by-layer assembled nanofilms of polyaniline (PANI) and maghemite (γ-Fe2O3—7.5-nm diameter) were probed with cross-sectional transmission electron microscopy (TEM) and magnetization measurements (magnetic hysteresis loops, magnetization using zero-field cooled/field-cooled protocols, and ac magnetic susceptibility). Additionally, simulations of the as-produced samples were performed to assess both the nanofilm’s morphology and the corresponding magnetic signatures using the cell dynamic system (CDS) approach and Monte Carlo (MC) through the standard Metropolis algorithm, respectively. Fine control of the film thickness and average maghemite particle–particle within this magnetic structure was accomplished by varying the number of bilayers (PANI/γ-Fe2O3) deposited onto silicon substrates or through changing the concentration of the maghemite particles suspended within the colloidal dispersion sample used for film fabrication. PANI/γ-Fe2O3 nanofilms comprising 5, 10, 25 and 50 deposited bilayers displayed, respectively, blocking temperatures (T B) of 30, 35, 39 and 40 K and effective energy barriers (ΔE/k B) of 1.0 × 103, 2.3 × 103, 2.8 × 103 and 2.9 × 103 K. Simulation of magnetic nanofilms using the CDS model provided the internal morphology to carry on MC simulation of the magnetic properties of the system taking into account the particle–particle dipolar interaction. The simulated (using CDS) surface–surface particle distance of 0.5, 2.5 and 4.5 nm was obtained for nanofilms with thicknesses of 36.0, 33.9 and 27.1 nm, respectively. The simulated (using MC) T B values were 33.0, 30.2 and 29.5 K for nanofilms with thicknesses of 36.0, 33.9 and 27.1 nm, respectively. We found the experimental (TEM and magnetic measurements) and the simulated data (CDS and MC) in very good agreement, falling within the same range and displaying the same systematic trend. Our findings open up new perspectives for fabrication of magnetic nanofilms with pre-established (simulated) morphology and magnetic properties.