Pectinolytic enzymes are related enzymes that hydrolyze pectic substances. Pectinolytic enzymes are of great interest in industrial applications for softening fruits, extracting and clarifying juices, extracting olive oil, retting textile fibers, preparing gel, and isolating protoplasts. The current work presents acidic extracellular pectinase production using low-cost agro-industrial waste with the indigenously isolated novel strain Aspergillus cervinus. Two fungal isolates, ARS2 and ARS8, with maximum pectinase activity, 41.88 ± 1.57 IU/mL and 39.27 ± 1.14 IU/mL, respectively, were screened out of 27 isolates from decayed fruit peels (orange, banana, and lemon) and soil containing decomposed vegetables. The isolate ARS2, identified as Aspergillus cervinus by molecular characterization, showed the highest pectinase activity of 43.05 ± 1.38IU/mL during screening and was further used for media component screening and optimization studies. To understand their effect on pectinase activity, one-factor-at-a-time (OFAT) studies were conducted on carbon sources, nitrogen sources, and mineral salts. The OFAT results showed the highest pectinase activity for orange peel (carbon source) at 44.51 ± 1.33 IU/mL, peptone (nitrogen source) at 45.05 ± 1.04 IU/mL, and NaH2PO4 (mineral salts) at 43.21 ± 1.12 IU/mL. The most significant media components screened by the Plackett–Burman (PB) design based on the p-value, Pareto chart, and main effect plot, were orange peel (p < 0.001), peptone (p < 0.001), NaH2PO4 (p < 0.001), and KH2PO4 (p < 0.001), which were further optimized using Response Surface Methodology (RSM) and Central Composite Design (CCD). The optimization results for the media components showed a maximum pectinase activity of 105.65 ± 0.31 IU/mL for 10.63 g orange peel, 3.96 g/L peptone, 2.07 g/L KH2PO4, and 2.10 g/L NaH2PO4. Thus, it was discovered that the indigenously isolated novel strain Aspergillus cervinus ARS2 was able to successfully produce a significant amount of pectinase using agro-industrial waste. Therefore, it can be considered for the large-scale optimized production of pectinase to meet industrial demands.