Perfluorooctanoic acid (PFOA) is a pervasive environmental contaminant with well-documented toxic effects on both humans and animals, attracting significant scientific concern. Due to its affinity for proteins, research has predominantly focused on PFOA's interactions with biological macromolecules. However, the specific role of smaller molecules, such as amino acids, remains underexplored. This study uniquely evaluates the potential of l-tryptophan (L-Trp) to mitigate PFOA toxicity and investigates the interaction mechanisms involved. Results indicate that the presence of L-Trp in PFOA-contaminated water reduces acute toxicity in Daphnia magna, with an optimal molar ratio of approximately 1:2 (Trp:PFOA). The findings reveal that non-covalent interactions, particularly van der Waals forces and hydrogen bonds, are central to the Trp–PFOA complex formation. Additional contributions from hydrophobic interactions at the indole group and electrostatic forces between carbonyl and amine groups further stabilize the complex. These interactions likely reduce PFOA's toxicity by altering its bioavailability and distribution. While this study offers valuable insights into the binding mechanisms between L-Trp and PFOA, it raises important questions about the reversibility of this interaction and its applicability to other per- and polyfluoroalkyl substances (PFASs).