SIRT3 modulates reactive oxygen species and helps to reduce oxidative stress, resulting in a neuroprotective effect in Parkinson’s disease. The work seeks to develop and synthesize novel, effective SIRT3 modulators, which will modify SIRT3 expression and generate the neuroprotective effect by downregulating reactive oxygen species. The synthesis of the new indole-based carboxamide derivatives IMW 1–16 was guided by molecular docking experiments with the SIRT3 wild-type protein. FT-IR, 1H-NMR, 13C-NMR, and mass spectrometry analyzed the synthesized compounds. The efficacy of the compounds IMW 1–16 was assessed using in-vitro assays such as the MTT assay, neuroprotection assay, lactate dehydrogenase assay, superoxide dismutase assay, glutathione peroxidase assay, reactive oxygen species estimation, mitochondrial membrane potential, and real-time polymerase chain reaction estimation. The synthesized compounds IMFW-1, IMTW-5, and IM24DCW-16 were determined to have the lowest cytotoxicity and the most neuroprotective effect. They were found to downregulate the lactate dehydrogenase enzyme levels. The compounds efficiently increased the expression of superoxide dismutase and glutathione peroxidase. They were shown to be beneficial in reducing reactive oxygen species levels. The compounds also significantly increased the expression of SIRT3, PGC-1α, and FOXO3, which are crucial for detoxifying reactive oxygen species. The synthesized novel indole-based carboxamide derivatives were effective modulators of SIRT3. Upregulating SIRT3 expression also upregulated other supporting proteins such as PGC-1α, SOD2, GPx, and FOXO3, and these targets have been known to downregulate the reactive oxygen species levels. The study’s findings reveal the therapeutic potential of the developed and synthesized compounds and their involvement in such pathological situations; among all the compounds, IM24DCW-16 was discovered to be the most promising candidate for the modulation of the SIRT3 in PD.