Two novel BODIPY dyes, BOC3 and BC12, were synthesized with variable alkyl chains at terminal amide functional units. BC12, featuring a longer alkyl chain (−C12H25), formed a gel compared to BOC3, which has a shorter alkyl chain (CH2OCH3), due to supra molecular self-assembly in film. Both dyes exhibited absorption peaks around 530 nm in the visible region, with a red shift of about 30 nm in the film state, essential for organic electronic applications. Concentration variation studies revealed π-π stacking/aggregates in the solid state causing red shifts in absorption and emission. BC12 exhibited more significant red shifts in film compared to its solution state due to supra molecular self-assembly. Electronic structure analysis using density functional theories (BMK and O3LYP) showed better correlation with absorption using the O3LYP method. Both dyes displayed quasi-irreversible oxidation and reduction couples with suitable HOMO (5.46 eV) and LUMO (3.32 eV) energy levels for organic electronic applications. Transient photoluminescence studies indicated a longer lifetime for BC12 (5.28 ns) than BOC3 (4.50 ns), suggesting π-π aggregation and supra molecular self-assembly. BC12′s gelation, attributed to its long alkyl chain and two-dimensional motifs of the BODIPY core, forms spherical-shaped nano networks. These findings underscore the potential of molecularly tuned dyes with alkyl chains for nano-sized self-assembly in organic electronic devices. Red shifts were observed due to combination of aggregation, stacking and columnar meso-phase formation in supramolecular assembly. Absorption spectra of dyes in toluene with various concentrations showed the formation of Aggregation/π-π stacking might be due to head to tailing interactions.