Disclosed is a stable formulation based on rAFP conjugated with drug delivery system of various classes of pharmacological agents such as dactinomycin, cardionolide, and bufadinolide, among others. In another embodiment, the invention discloses a method of producing rAFP in a strain of methylotrophic Pichia pastoris yeast, allowing the yeast to replicate, and extracting the newly created rAFP. The method provides a nonpyrogenic, highly stable, recombinant, fully refolded rAFP and its fragments that are free from stable folding intermediates caused by non-native disulfide bridges and irreversible aggregates. The newly created rAFP is purified using a two-step chromatographic purification process in the presence of 0.5% polysorbate-20 and 10 mM inosine that prevents aggregation of the monomers of the target protein, increasing the yield of biologically active rAFP. The invented formulation of rAFP is conjugated with active pharmacological substances or target drug delivery system for prevention or treatment of oncological and autoimmune-diseases.