Lockyer became a clerk in the War Office in 1857, but his interest in astronomy eventually led to a career in that field. He initiated in 1866 the spectroscopic observation of sunspots (sunspot), and in 1868 he found that solar prominences (solar prominence) are upheavals in a layer around the Sun, which he named the chromosphere. Also in 1868, he and Pierre Janssen, working independently, discovered a spectroscopic method of observing solar prominences without the aid of an eclipse to block out the glare of the Sun. Lockyer identified the element helium in the solar spectrum 27 years before that element was found on the Earth.

Between 1870 and 1905, Lockyer conducted eight expeditions to observe solar eclipses. He also built a private observatory at Sidmouth and theorized on stellar evolution. A prolific writer, he founded the science periodical Nature in 1869 and edited it until a few months before his death. He was knighted in 1897.