Amyotrophic lateral sclerosis (ALS) is a fatal, currently incurable neurodegenerative disease that progressively affects the upper motor neurons in the brain and lower motor neurons in the spinal cord. A significant portion of patients exhibit abnormalities in lipid metabolism, which appear to contribute to denervation and subsequent motor neuron degeneration. This study aimed to computationally identify lipid-based compounds associated with ALS and elucidate their pathological and therapeutic roles to facilitate effective ALS diagnosis and treatment. The methodologies employed encompassed rational database searches, pharmacokinetic and target predictions, as well as docking and molecular dynamics simulations (MDS). The findings from the disease-to-lipids analysis identified 20 lipid compounds correlated with ALS, primarily categorized as potential inhibitors within the functional classes of vitamins, antibiotics, organic acids, and phytochemicals. Pharmacokinetic predictions revealed that only four compounds exhibited permeability across the blood–brain barrier, namely 4-hydroxynonenal, resveratrol, rotenone, and valproic acid. Docking simulations indicated the highest binding affinity for 4-hydroxynonenal with alkaline ceramidase 2 (−4.516 kcal/mol), resveratrol with carbonic anhydrase 6 (−7.070 kcal/mol), rotenone with cytochrome P450 2C19 (−7.378 kcal/mol), and valproic acid with glutamate carboxypeptidase 2 (−5.629 kcal/mol). Furthermore, MDS and molecular mechanics/generalized born surface area calculations demonstrated the stability and binding energies of the complexes under simulated physiological conditions. In summary, further investigation is warranted to explore the synergistic effects of resveratrol and valproic acid in ALS, the mechanisms underlying 4-hydroxynonenal adduct-assisted aggregate formation of certain enzymes in ALS, and the impact of prolonged human exposure to rotenone from marine food sources (such as fish) on the development of ALS.