Background/Objectives: Melanoma malignum is considered the most dangerous form of skin cancer, characterized by the exceptional resistance to many conventional chemotherapies. The aim of this study was to evaluate the effect of NutramilTM Complex (NC)—Food for Special Medical Purpose (FSMP), on two types of melanoma cell lines, primary WM115 and malignant WM266-4. Methods: At 24 h after seeding, growth medium was replaced with a medium containing encoded treatments of NC or NC-CC (NutramilTM Complex without calcium caseinate) at various concentrations. Cells were treated for 24, 48, and 72 h. Results: Our results showed that NutramilTM Complex reduces proliferation of malignant melanoma WM266-4 cells but did not affect the proliferation of WM115 primary melanoma. This was followed by measured down-regulation of selected pro-survival proteins expression in WM266-4 cells, specifically ERK1/2, AKT-1, HSP27, Survivin, and TAK1. Interestingly, our results showed elevated levels of some pro-apoptotic proteins in both cell lines, including Bad, Smad2, p38MAPK, cleaved forms of Caspase-3/7, as well as cleaved PARP. Conclusions: Taken together, our results indicate that various melanoma cancer cell lines may respond in a different way to the same compound. They also suggest induction of apoptotic pathway by NutramilTM Complex as the most likely mechanism of its anticarcinogenic activity.