Originally designated as a flotilla leader and a torpedo cruiser in Decker's Fleet Plan of 1931, she was hastily commissioned on 10 May 1940, when Germany invaded the Netherlands.

The ship was meant to commence trials on the day the Germans invaded, and to prevent her capture the Jacob van Heemskerck was immediately pressed into service.

At the end of the month, Jacob van Heemskerck and the cruiser HNLMS Sumatra received the assignment to transport Princess Juliana and her two children (including the later Beatrix of the Netherlands) to Canada.

Jacob van Heemskerck returned alone to England and arrived at Portsmouth in July where her re-arming programme began.

On 28 November 1942, Jacob van Heemskerck, in the company of the Australian cruiser HMAS Adelaide, identified and intercepted the German supply vessel and blockade runner Ramses in the Indian Ocean while posing as a Norwegian ship; the German freighter was subsequently scuttled by her own crew and finished off by the Allied warships.