Nowowiejski was born in Wartenburg (today Barczewo) in Warmia in the Prussian Partition of Poland (then administratively part of the Province of East Prussia, German Empire).

While Franz Adam Nowowiejski enthusiastically promoted Polish culture, Feliks's mother displayed a strong interest in the arts, particularly as a pianist.

With her participation in performances of Polish folk songs and recitations of noted poets from Poland and Germany as well as her own poetry, she fostered the formidable musical talent of her son, likely an inheritance from her.

Thanks to a composition prize for his march Pod sztandarem pokoju (Under the Banner of Peace), he was able to study at the Stern Conservatory from April to September 1898.

After submitting a cantata to the Royal Academy of Arts, Berlin, he was accepted into a master class for composition under Max Bruch from 1900 to 1902.

For his oratorio Powrót syna marnotrawnego (Return of the Prodigal Son), Nowowiejski won his first Giacomo Meyerbeer Prize.

With the 4,500 marks of prize money, he financed an educational tour of Germany, Bohemia, Moravia, Austria, Italy, Africa, France and Belgium, during which he met Gustav Mahler, Camille Saint-Saëns, Pietro Mascagni and Ruggero Leoncavallo.

After its Amsterdam premiere in 1909, the oratorio was performed in more than 150 cities in Europe, and North and South America, securing Nowowiejski's international reputation.

On 15 July 1910 - the 500th anniversary of the Battle of Grunwald - the citizens of Krakow gathered in Jan Matejko Square to sing the Rota by Maria Konopnicka under Nowowiejski's direction.

In 1910, with his piece Zagasły już (Extinguished), Nowowiejski took first prize in a Lwów composing competition commemorating the 100th birthday of Frédéric Chopin.

During the German invasion of Poland at the start of World War II in 1939, Nowowiejski hid first among the nuns of St. Elizabeth's Hospital in Poznań, afterwards fleeing to Kraków.

After World War II, when the region of Warmia became again part of Poland, Nowowiejski was seen increasingly as a Pole due to his pro-Polish views and Polish themes in so many of his works.