We prove the first rigorous bound on the heat transfer for three-dimensional Rayleigh-Bénard convection of finite-Prandtl-number fluids between free-slip boundaries with an imposed heat flux. Using the auxiliary functional method with a quadratic functional, which is equivalent to the background method, we prove that the Nusselt number $Nu$ is bounded by $Nu \leq 0.5999 R^{1/3}$ uniformly in the Prandtl number, where $R$ is the Rayleigh number based on the imposed heat flux. In terms of the Rayleigh number based on the mean vertical temperature drop, $Ra$, we obtain $Nu \leq 0.4646 Ra^{1/2}$. The scaling with Rayleigh number is the same as that of bounds obtained with no-slip isothermal, free-slip isothermal, and no-slip fixed flux boundaries, and numerical optimisation of the bound suggests that it cannot be improved within our bounding framework. Contrary to the two-dimensional case, therefore, the $Ra$-dependence of rigorous upper bounds on the heat transfer obtained with the background method for three-dimensional Rayleigh-Bénard convection is insensitive to both the thermal and the velocity boundary conditions.