Boltwood, the son of a lawyer, was born in Amherst, Massachusetts, and educated at Yale and the University of Munich. Apart from the period 1900–06, when he served as a private consultant, and the year 1909–10, which he spent in England with Ernest Rutherford at the University of Manchester, he devoted the whole of his academic career to Yale. He occupied the chair of physics (1906–10), the chair of radioactivity (1910–18), and the chair of chemistry from 1918 until his death by suicide in 1927.

Boltwood made a number of contributions to the study of radioactivity. The radioactivity of uranium and radium had been discovered in the 1890s by Henri Becquerel and Marie Curie. Starting in 1902 Rutherford and Frederick Soddy had shown that radium, uranium, and other radioactive elements broke down in a quite complicated sequence into other elements. Boltwood worked on the breakdown of uranium into radium, a process that Soddy had not found easy to demonstrate. Soddy had tried to obtain radium directly from uranium in 1904 and failed. Boltwood postulated that this was because uranium did not decay directly into radium but into some intermediate element, and began to search for it. After much effort Boltwood eventually found what he was looking for in ‘actinium X’, which, as it appeared different from anything else, he felt confident enough to claim as a new element and named it ‘ionium’ in 1907. This claim ran into trouble when ionium was found to behave very much like thorium and in 1908 it was shown by B. Keetman that if ionium and thorium are mixed together no chemical technique can separate them. Soddy decided the matter in 1913 when he was able to obtain a spectrograph of ionium and found it to be the same as thorium. Although he was wrong in detail, the general picture Boltwood had developed of the decay of uranium to radium was valid until superseded by Soddy's idea of the isotope.

One important byproduct of Boltwood's work was his demonstration in 1905 that lead was always found in uranium and was probably the final stable product of its decay. He argued that in minerals of the same age the lead–uranium ratio would be constant, and in minerals of different ages the ratio would be different. He calculated some estimates of the ages of several rocks based on the estimates then accepted for decay rates and came up with some good results. This was the beginning of attempts to date rocks and fossils by radiation measurements and other physical techniques, which have so revolutionized geology and archeology.