This paper addresses a computational method aimed at obtaining the isothermal compressibility of ferrofluids by means of molecular dynamics (MD) simulations. We model ferrofluids as a system of dipolar soft spheres and carry out MD simulations in the NPT ensemble. The obtained isothermal compressibility computed via volume fluctuations provides us with a strong evidence that dipolar interactions lead to a higher compressibility of dipolar soft sphere systems: the stronger the dipolar interactions, the bigger is the deviation of the compressibility from the one of a system with no dipoles. Furthermore, we use the isothermal compressibility to calculate the structure factor of ferrofluids at low values of wave vectors, i.e. in the range where it is difficult to predict its behaviour because of a problem with accounting for long-range particle correlations that give the main contribution to the structure factor in this range. Our approach based on the interpolation of the structure factor and the computed isothermal compressibility allows us to obtain the smooth structure factor in the range of low wave vectors and the reliable fractal dimension of the clusters formed in the system.