1,4-Butanedithiol is primarily used in the field of organic synthesis, where it serves as a building block for creating more complex molecules. Its dual thiol groups make it a valuable reagent for forming sulfur-containing compounds, which are often used in pharmaceuticals, agrochemicals, and materials science.

In materials science, it is employed as a crosslinking agent in the production of polymers and elastomers, enhancing their mechanical properties and durability. Additionally, it finds application in the preparation of self-assembled monolayers (SAMs) on gold surfaces, which are crucial in nanotechnology and surface chemistry for creating highly ordered molecular structures.

The compound is also utilized in the synthesis of ligands for metal coordination chemistry, aiding in the development of catalysts and metal-organic frameworks (MOFs). Its ability to bind to metal ions makes it useful in various catalytic processes and in the study of metal-ligand interactions.

In the field of biochemistry, 1,4-butanedithiol is sometimes used in the modification of proteins and peptides, particularly in the formation of disulfide bonds, which are essential for the stability and function of many proteins. This application is important in the development of bioconjugates and in the study of protein folding and structure.