In 1814, Jean-Jacques Colin discovered (to his surprise) that a mixture of dry gaseous ammonia and iodine formed a shiny, metallic-appearing liquid. Frederick Guthrie established the precise composition of the resulting I···NH complex fifty years later, but the physical processes underlying the molecular interaction remained mysterious until the development of Robert S. Mullikens theory of inner-sphere and outer-sphere interactions.  In Mullikens categorization, the intermolecular interactions associated with small partial charges affect only the "inner sphere" of an atom's electron distribution; the electron redistribution associated with Lewis adducts affects the "outer sphere" instead.
Then, in 1954, Odd Hassel fruitfully applied the distinction to rationalize the X-ray diffraction patterns associated with a mixture of 1,4-dioxane and bromine. The patterns suggested that only 2.71 Å separated the dioxane oxygen atoms and bromine atoms, much closer than the sum (3.35 Å) of the atoms' van der Waals radii; and that the angle between the O&minus;Br and Br&minus;Br bond was about 180°.  From these facts, Hassel concluded that halogen atoms are directly linked to electron pair donors in a direction with a bond direction that coincides with the axes of the orbitals of the lone pairs in the electron pair donor molecule.  For this work, Hassel was awarded the 1969 Nobel Prize in Chemistry.
Dumas and coworkers first coined the term "halogen bond" in 1978, during their investigations into complexes of CCl, CBr, SiCl, and SiBr with tetrahydrofuran, tetrahydropyran, pyridine, anisole, and di-n-butyl ether in organic solvents.
However, it was not until the mid-1990s, that the nature and applications of the halogen bond began to be intensively studied.  Through systematic and extensive microwave spectroscopy of gas-phase halogen bond adducts, Legon and coworkers drew attention to the similarities between halogen-bonding and better-known hydrogen-bonding interactions.
In 2007, computational calculations by Politzer and Murray showed that an anisotropic electron density distribution around the halogen nucleus — the "σ-hole" — underlay the high directionality of the halogen bond. This hole was then experimentally observed using Kelvin probe force microscopy.
In 2020, Kellett et al. showed that halogen bonds also have a π-covalent character similar to metal coordination bonds. In August 2023 the "π-hole" was too experimentally observed