The use of natural antimicrobial products has increased in recent years, including plant extracts with potential activity against fish pathogen bacteria. These phytocompounds constitute an alternative to decrease the use of antibiotics that frequently cause bacterial resistance and can be harmful to the environment. Numerous studies using phytogenic compounds from Andrographis paniculata have previously shown promising anti-biofilm and antimicrobial properties on Pseudomonas aeruginosa, Klebsiella pneumoniae and in Streptococcus agalactiae infections in Nile tilapia (Oreochromis niloticus). In this sense, our previous work reported the protective effect of A. paniculata on SHK-1 Salmo salar macrophage cells and fish infected with P. salmonis. A. paniculata belongs to the Acanthaceae family and is a popular ancient medicinal herb used to treat several diseases in many Asian countries, including India. Andrographolide is the major labdane diterpenoid isolated from A. paniculate, which has been reported to exhibit antibacterial, anti-inflammatory and anticancer activities both in vitro and in vivo. In this study, we demonstrated that Andrographolide decreases the florfenicol MICs on P. salmonis from 0.5 to 0.25 μg/mL in SHK-1 cells. This effect on the florfenicol action was corroborated through the LDH measurement in the cellular supernatant subjected to the different doses, which demonstrated the synergy between Andrographolide and the antibiotic in the range of 0.125; 0.25 and 0.5 μg/mL. In addition, the transcriptomic analysis performed on the SHK-1 cells treated with Andrographolide demonstrated a significant modulation of different cellular processes. The quantification of DEGs and subsequent analysis revealed a higher number of downregulated genes in the Andrographolide supplemented cell group, with a 2:1 ratio compared to upregulated genes. The data for the general analysis shows two primary clusters: macromolecule biosynthetic processes and RNA processing pathways. These are accompanied by secondary clusters involving blood vessel development and negative regulation of metabolic processes. A noteworthy observation is that RNA processing forms the central organizing hub for downregulated genes, mirroring its role as the second most significant network in the general enrichment analysis. Additionally, shared features between the general and downregulated analyses include chromatin organization and ATP-dependent chromatin remodeling activities. In contrast, the upregulated gene network demonstrates minimal overlap with the general analysis, with blood vessel development standing out as the only common node. The upregulated genes appear to contribute to more specialized functions through their distinct, less integrated network configuration. The downregulation of RNA processing, nucleic acid metabolic process versus the upregulation of amino acid metabolic processes and histone h4 kinase activity may indicate a decrease in the biogenesis in the Andrographolide supplement group, while the increase of upregulated processes may indicate changes in metabolism. These findings, associated with synergic effect on florfenicol action against P. salmonis and transcriptomic modulation in SHK-1 cells, suggest the multidimensional effect of Andrographolide on fish immune cells and support its application as a functional additive in fish diets.