Perfluoro-1-iodohexane is primarily used in the field of organic synthesis as a building block for creating more complex fluorinated compounds. Its strong carbon-iodine bond makes it a valuable reagent in nucleophilic substitution reactions, enabling the introduction of perfluoroalkyl groups into various organic molecules. This property is particularly useful in the development of pharmaceuticals, agrochemicals, and specialty materials where fluorinated compounds are desired for their stability and unique chemical properties.

In materials science, it serves as a precursor for the production of fluoropolymers and surfactants. These materials are often employed in applications requiring high thermal stability, chemical resistance, and low surface energy, such as coatings, lubricants, and water-repellent treatments. Additionally, its use in the synthesis of fluorinated surfactants contributes to the creation of firefighting foams and industrial cleaning agents.

In research and development, perfluoro-1-iodohexane is utilized as a model compound to study the behavior of perfluoroalkyl iodides in various chemical reactions. This helps in advancing the understanding of fluorinated organic chemistry and in designing novel fluorinated materials with tailored properties.