After being appointed in 1891 as second lieutenant in the First field artillery regiment and spending some time in the cavalry school in Ypres, he passed the officer examination of the École Polytechnique for the French Navy.

[2][3] This three-year detachment was exceptional and happened as a result of an audience with king Leopold II: it was only granted to one other Belgian officer, but refused to his friend Emile Danco.

For this achievement, he received the Légion d’Honneur in France which the Belgian King Leopold II allowed him to use in Belgium.

[6] It must be remembered that the Belgica's company was as cosmopolitan as it could be, and it was the business of the second in command to keep all these men together and get the best possible work out of them.Lecointe acquitted himself admirably; amiable and firm, he secured the respect of all.

He had also won his "nautical" spurs on the voyages he had made, including a number to the Far East in the French navy [17].De Gerlache offered him the position once more in 1897 as second-in-command of the expedition.

Despite de Gerlache's misgivings, they cajoled the sick expedition members into eating fresh seal and penguin meat, nursing them back to health.

Lecointe, jointly with Cook and Amundsen, drafted a detailed plan to reach the South Magnetic Pole in 1899–1900; this was discussed on board during the period of August to November 1898.

On reaching South America Lecointe started exploring the Andes while de Gerlache sailed the Belgica back to Belgium.

He served as its vice-president from 1919 to 1922,[13] and lead its Central Bureau for Astronomical Telegrams from 1920 to 1922, while it was temporarily located in Uccle following the First World War.

[14] In 1919 he was elected to the executive committee of the International Research Council at its founding congress in Brussels, together with Schuster, Volterra and Hale, with Picard as president.