The dynamics of the conjugated polymers poly(9,9-dioctylfluorene) (PF8) and poly(9,9-didodecylfluorene) (PF12), differing by the length of their side chains, is investigated in the amorphous phase using the temperature-dependent quasielastic neutron scattering (QENS) technique. The neutron spectroscopy measurements are synergistically underpinned by molecular dynamics (MD) simulations. The probe is focused on the picosecond time scale, where the structural dynamics of both PF8 and PF12 would mainly be dominated by the motions of their side chains. The measurements highlighted temperature-induced dynamics, reflected in the broadening of the QENS spectra upon heating. The MD simulations reproduced well the observations; hence, the neutron measurements validate the MD force fields, the adopted amorphous model structures, and the numerical procedure. As the QENS spectra are dominated by the signal from the hydrogens on the backbones and side chains of PF8 and PF12, extensive analysis of the MD simulations allowed the following: (i) tagging these hydrogens, (ii) estimating their contributions to the self-part of the van Hove functions and hence to the QENS spectra, and (iii) determining the activation energies of the different motions involving the tagged hydrogens. PF12 is found to exhibit QENS spectra broader than those of PF8, indicating a more pronounced motion of the didodecyl chains of PF12 as compared to dioctyl chains of PF8. This is in agreement with the outcome of our MD analysis: (i) confirming a lower glass transition temperature of PF12 compared to PF8, (ii) showing PF12 having a lower density than PF8, and (iii) highlighting lower activation energies of the motions of PF12 in comparison with PF8. This study helped to gain insights into the temperature-induced side-chain dynamics of the PF8 and PF12 conjugated polymers, influencing their stability, which could potentially impact, on the practical side, the performance of the associated optoelectronic active layer.