Algae-derived phytochemicals have potential as novel and sustainable therapeutic agents. The exploration of these naturally occurring bioactive compounds is necessary to tap their unrealized potential for the advancements in the field of drug discovery. The traditional drug discovery process faces many challenges including high failure rate, cost, and environmental hazards, while phytochemicals as bioproducts hold promising eco-friendly solutions. In this chapter, we will explore how integrated computational and experimental approaches can be applied to accelerate the drug discovery process from algal-derived bioactive compounds. We will also explore in depth the techniques such as high-throughput virtual screening (HTVS), molecular docking, ADMET (absorption, distribution, metabolism, excretion, and toxicity) assessment, molecular dynamics (MD) simulation, as well as modern in-vitro extraction techniques such as ultrasonic-assisted extraction (UAE). This chapter provides comprehensive insights into various computational tools for each method, including their strengths and limitations. This chapter also draws attention to purification processes such as column chromatography and compound characterization through spectrometry. The discussion addresses key challenges including environmental considerations and technical limitations while presenting innovative approaches. Overall, this chapter provides a roadmap for researchers in the field of marine biotechnology, pharmaceutical science, and other drug-discovery-related fields for harnessing sustainable, therapeutically potential algal phytochemicals utilizing modern bioinformatics tools complete with practical guidelines and methodological frameworks for implementation.