* He was the eponym of the Lyman series of spectral lines. 
* The crater  Lyman on the far side of the Moon is named after him. 
* He was elected to the American Academy of Arts and Sciences in 1901.
* He was elected to the United States National Academy of Sciences in 1917.
* He was elected to the American Philosophical Society in 1918.
* He was awarded the Franklin Institute's Elliott Cresson Medal in 1931.
* The Lyman Laboratory of Physics at Harvard University is named after him.