We provide numerical evidence that a Kelvin-Helmholtz instability occurs in the Dirac fluid of electrons in graphene and can be detected in current experiments. This instability appears for electrons in the viscous regime passing though a micrometer-scale obstacle and affects measurements on the time scale of nanoseconds. A possible realization with a needle-shaped obstacle is proposed to produce and detect this instability by measuring the electric potential difference between contact points located before and after the obstacle. We also show that, for our setup, the Kelvin-Helmholtz instability leads to the formation of whirlpools similar to the ones reported in Bandurin et al. [Science 351, 1055 (2016)]. To perform the simulations, we develop a lattice Boltzmann method able to recover the full dissipation in a fluid of massless particles.