Born at Zoerle-Parwijs, near Westerlo, Belgium, Lemmens took lessons from François-Joseph Fétis, who wanted to make him into a musician capable of renewing the organ-player's art in Belgium. Fétis sent him to Adolf Friedrich Hesse in Germany to learn Johann Sebastian Bach's tradition.

In 1847, Lemmens won the Paris Conservatoire's prestigious Prix de Rome with his Le roi Lear ("King Lear"). One year later he published his first work for organ: Dix improvisations dans le style sévère et chantant ("Ten improvisations in a strict and singing style"). In March 1849 he was appointed organ teacher at the Royal Brussels Conservatoire, aged only 26; and he trained numerous young musicians, including two eminent Frenchmen, Alexandre Guilmant and Charles-Marie Widor.

During 1852 he gave organ recitals in Saint Vincent de Paul, La Madeleine and Saint Eustache churches in Paris, where he stunned audiences with his technique. Particularly notable was his brilliant pedal-playing, which owed a good deal to his studies of Bach's music (at the time Bach's organ works were not at all well known in France). In 1857 he married the English soprano Helen Sherrington (1834–1906), who in the following decade emerged as a leading English concert and operatic singer. He died at Zemst, near Mechelen, Belgium.