Nocturnal asthma (NA) is a high-prevalence disease that causes severe respiratory issues, leading to death from early midnight to early morning. In this research, nanoparticulate drug delivery system of methylprednisolone (MP) was developed using chitosan (CH) and pectin (PEC). MP is a synthetic corticosteroid medication widely used for its potent anti-inflammatory activity. Computational simulation study (AI-based blend analysis algorithm) was used to identify a better-mixing polymer with MP. MP nanoparticles were formulated by the ionic gelation method with the combination of CH and PEC. To modify the drug release properties, the formed beads were coated with chitosan succinate (CSSC). The morphological characteristics of the beads were determined by SEM analysis. The X-ray radiographic imaging study was used to observe the intactness of MP beads. Histopathological studies were also carried out to find out the toxicity of the beads in the organs of rats. Pectin and chitosan polymers were selected based on the computational simulation study. SEM analysis revealed that the beads had a spherical shape with a rough outer surface. CSSC-coated beads achieved sustained drug release for up to 24 h. X-ray imaging demonstrated the stability of the beads in acidic pH conditions. In vivo pharmacokinetic studies showed that CSSC-coated beads were more stable in the gastrointestinal tract (GIT) than PEC-CH beads and the pure drug. Histological evaluation confirmed that the beads are nontoxic and safe for use in rats. Based on the findings, it was concluded that CSSC-coated beads of MP exhibited superior release properties, making them suitable for a chronomodulated drug delivery system.