The unclear miscibility of CuNi alloys was investigated with atom probe tomography (APT). Multilayered thin film samples were prepared by ion beam sputtering (IBS) and focused ion beam (FIB) shaping. Long-term isothermal annealing treatments in a UHV furnace were conducted at temperatures of 573, 623, and 673 K to investigate the mixing process. The effective interdiffusion coefficient of the nanocrystalline microstructure (including defect diffusion) was determined to be Deff = 1.86 × 10−10 m2/s × exp(−164 kJ/mol/RT) by fitting periodic composition profiles through a Fourier series. In nonequilibrium states, microstructural defects like grain boundaries and precipitates were observed. While at the two higher temperatures total mixing is observed, a clear experimental evidence is found for a miscibility gap at 573 K with the boundary concentrations of 26 and 66 at%. These two compositions are used in a subregular solution model to reconstruct the phase miscibility gap. So, the critical temperature TC of the miscibility gap is found to be 608 K at a concentration of 45 at% Ni.