In this article, we analyse a stabilised equal-order finite element approximation for the Stokes equations on anisotropic meshes. In particular, we allow arbitrary anisotropies in a sub-domain, for example along the boundary of the domain, with the only condition that a maximum angle is fulfilled in each element.This discretisation is motivated by applications on moving domains as arising e.g. in fluid-structure interaction or multiphase-flow problems. To deal with the anisotropies, we define a modification of the original Continuous Interior Penalty stabilisation approach. We show analytically the discrete stability of the method and convergence of order ${cal O}(h^{3/2})$ in the energy norm and ${cal O}(h^{5/2})$ in the $L^2$-norm of the velocities. We present numerical examples for a linear Stokes problem and for a non-linear fluid-structure interaction problem, that substantiate the analytical results and show the capabilities of the approach.