Janssen studied mathematics and physics at Paris university before becoming professor of general science at the school of architecture. In 1857 he went to Peru to determine the magnetic equator. He observed the transits of Venus of 1874 and 1882 in Japan and Algeria and went on all the major eclipse expeditions. So keen was he to witness the 1870 eclipse in Algeria that he had to escape from the siege of Paris by balloon. While in India in 1868, observing the solar eclipse spectroscopically, he noticed the hydrogen lines visible in the solar prominences and wondered if they could still be detected after the eclipse. The next day he found them still visible. This meant that while photography and observation would still depend on eclipse work the spectroscope could be used almost anywhere anytime. Janssen made one further important discovery on the same trip; he discovered lines in the solar spectrum that he could not identify. He sent his results to Norman Lockyer who suggested that they were produced by some element found only on the Sun, which Lockyer named helium. In 1895 William Ramsay discovered a substance on Earth that matched exactly with Janssen's spectral lines.

In later life Janssen arranged for an observatory to be built on Mont Blanc to avoid as much atmospheric interference as possible. Using data from observations made there, he showed that absorption lines in the solar spectrum are caused by elements in the Earth's atmosphere.