Each unit cell in YBa$_2$Cu$_3$O$_{6+x}$ contains a pair of two-dimensional CuO$_2$ layers. While the crystal structure is globally inversion symmetric, the individual layers are not. This leads, necessarily, to a nonvanishing Rashba spin-orbit coupling (SOC) in the CuO$_2$ layers, with opposite signs of the coupling constant in each layer. These so-called Rashba bilayers generate hidden spin textures, with a vansishing net spin at each $k$-point in the Brillouin zone, but nonvanishing spin textures in each layer separately. Here, we trace the microscopic origin of the Rashba splitting through the orbital structure of the CuO$_2$ conduction bands, obtain a generic three-orbital model Hamiltonian, and show that the magnitude of the spin-splitting predicted by density functional theory is $sim 10$~meV.