In the last decade, the Jensen inequality has been intensively used in the context of time-delay or sampled-data systems since it is an appropriate tool to derive tractable stability conditions expressed in terms of linear matrix inequalities (LMIs). However, it is also well-known that this inequality introduces an undesirable conservatism in the stability conditions and looking at the literature, reducing this gap is a relevant issue and always an open problem. In this paper, we propose an alternative inequality based on the Fourier Theory, more precisely on the Wirtinger inequalities. It is shown that this resulting inequality encompasses the Jensen one and also leads to tractable LMI conditions. In order to illustrate the potential gain of employing this new inequality with respect to the Jensen one, two applications on time-delay and sampled-data stability analysis are provided.