Around 1230, the town was no more than a core of a number of huts. After 1300 the place started to grow and it quickly became known for fishing, but also for inland shipping. In 1388 the fish market from Katwijk aan den Rijn was moved to Katwijk aan Zee. The two places were already under the same board, Katwijk, but then it was a glory. Katwijk aan Zee has been a well-known seaside resort since the 20th century. In the late 1960s Katwijk had the largest fishing fleet in the Netherlands with 180 ships. Later, when more modern ships arrived, the Katwijk ships diverted to the ports of IJmuiden and Scheveningen and the fleet became smaller.
During the Second World War, part of the buildings in Katwijk aan Zee were demolished by the Germans. It was a 200-meter-wide strip of houses along the coast, which had to disappear to make way for the Atlantic Wall. The boulevard only got its current appearance after the war.
At the end of the eighties, Katwijk aan Zee melted together with Katwijk aan den Rijn and the northern (new-build) districts of Hoornes and Rijnsoever, now Katwijk-Noord, into one large municipality, Katwijk. As of 1 January 2006, the surrounding villages of Rijnsburg and Valkenburg also fall under the municipality of Katwijk.