Born in Flensburg in 1868, Eckener earned a doctorate at the University of Leipzig before joining the Germany army Infantry Regiment. He subsequently worked as a journalist and editor. During his time as a journalist, Eckener covered the first flights of Zeppelins LZ-1 and LZ-2. Whilst he was critical of the airships' performance, he admired Graf von Zeppelin and subsequently discussed Zeppelin's plans with him. Eckener was so impressed that in October 1908 he agreed to become a part-time publicist for Zeppelin's company. Eckener's interest in airships grew to the extent that he joined the company full-time and obtained his airship licence in 1911.

When Graf von Zeppelin died in 1917, Eckener succeeded him at the head of Luftschiffbau Zeppelin. As he was prevented from constructing airships of the size needed for translatic flight under the terms of the Treaty of Versailles, Eckener lobbied both the German and US governments to allow the company to build a Zeppelin for the US navy as part of German's war reparations. The company went on to build LZ 126, later renamed the USS Los Angeles, which became the longest-serving rigid airship to operate in the US navy.

The next ship the company built under Eckener's leadership was the Graf Zeppelin, which became the most successful rigid airship ever. Eckener was at the helm of Graf Zeppelin during most of its record-setting flights, including the first intercontinental passenger airship flight in 1928 and the Graf Zeppelin's flight around in the world in 1929.

Eckener wanted to run against Hitler in the 1932 German presidential election, which angered the Nazi party to the point that when they came to power in 1933 they arrested Eckener. Despite his dislike for and regular criticism of the Nazis, Eckener survived the war. fter the Hindenburg crash he redesigned LZ 130 Graf Zeppelin II to work with helium but could not obtain it because of the geo-political situation at the time. After the war he tried to build large rigid airships with Goodyear Zeppelin Corporation but nothing came of that plan.

Eckener died in Friedrichshafen on 14 August 1954.