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Three different fluorine (4-CF3, 3,5-CF3 and 3,4,5-F) end-capped, A2–π–A1–π–A2 type small molecular non-fullerene acceptor molecules (1CFPzDP, 2CFPzDP, and 3FPzDP) containing a common central core acceptor, namely dipyrrolo[2,3-b:2′,3′-e]pyrazine-2,6(1H,5H)-dione (PzDP), have been synthesized and characterized. Density functional methods exhibit the distinct structural features of the PzDP unit upon comparison with benzodipyrrolidone (BzDP), i.e., the presence of electron rich heteroatoms from the pyrazine core of the PzDP unit increased the planarity of the molecular system through intra/intermolecular non-covalent bonding interactions. In this study, end-capped fluorination was introduced onto the PzDP unit to enhance the intermolecular interactions, oxidative stability, and charge mobility. Moreover, we have made an attempt to investigate the positional substitution effects of F and CF3 units on the optoelectronic properties. As envisaged, the synergistic combination of these two distinct individual functionalities into a single molecular system significantly increased the optoelectronic properties. DFT and TDDFT calculations substantiated the experimental observations by means of planarity, energy levels and charge transfer transitions. All the dyes exhibit two reduction potentials; the HOMO and LUMO values are measured to be −6.08/−4.05 eV, −6.21/−4.08 eV, and −6.09/−4.06 eV for 1CFPzDP, 2CFPzDP, and 3FPzDP, respectively. The energy levels are well-matched with regioregular poly(3-hexylthiophene-2,5-diyl) (P3HT) (−5.0/−3.0 eV), which can act as an n-type semiconductor for bulk heterojunction organic solar cell (BHJOSC) applications. Fluorescence quenching experiments revealed an efficient charge transfer between the donor material P3HT and the synthesized acceptor molecules. Td values of the dyes are in the range of 359–382 °C representing their good thermal stability. DFT calculations to obtain key photovoltaic parameters such as open-circuit voltage (Voc), exciton binding energy (Eb) and transition characteristics for the developed and reference acceptor systems have been performed. Based on the properties evaluated, these dyes are found to be promising electron acceptor candidates for the fabrication of BHJOSCs. [ABSTRACT FROM AUTHOR]