The earliest references to the lighthouse navigation at the mouth of the Narva River date back to Swedish times. It was mainly used by ships transporting timber, assisting them with locating the right anchorage near the river mouth in the darkness, as ships with a deeper draft could not pass through the shallow path of the river (wood itself was transported to the ships by boats). Nowadays, in Narva bay and along the river mouth, boats are navigated not only with lighthouse but also by luminous signs from the left side of the river. Narva-Jõesuu lighthouse is the easternmost lighthouse in Estonia.

The earliest references to the local lighthouse go as far back as 1725. However, the confirmed records of construction of the lighthouse is dated 1808, when a 16-metre-high limestone lighthouse with a low tower was erected. The height of the lantern room above sea level was 22 metres, and the visibility distance of the light was 14 miles. In the 1870s, the lighthouse was reconstructed, as the building was largely buried under storm sand and also technically outdated. By 1886, the structure of the tower had been strengthened and the tech equipment had been updated. The tower itself was higher, as was the lantern room – at a height of 24 metres. The lighthouse with its outbuildings was destroyed during the Second World War.

The new tower, which still stands today, was completed in 1957. It was built from prefab reinforced concrete semi-circle cylinders, which were manufactured in Tallinn and transported to Narva-Jõesuu as 1.5 ton parts. In addition, the outbuildings were also erected – two residential buildings, a generator building, a workshop, a sauna, etc. The visible distance of the red-and-white-striped tower was 17 miles, its height from the base was 31 metres, and the height of the light was 35 metres above sea level.