This research was performed with the purpose of investigating the effect of a magnetic field on the antipathogenic, antioxidant, and anticoagulant activities of purified phycocyanin (PC) from the cyanobacterium <i>Spirulina laxa</i>. Magnetic fields of 30 and 60 mT generated by an electric current and ferrite magnets were applied for 21 days. After biomass production and purification of PC, different analyses of antibacterial, antioxidant, and anticoagulant activity were performed. The results showed that magnetic fields of 30 mT showed the highest intensity of PC absorption. While the magnetic field of 60 mT caused the highest purity of PC compared to the control sample (<i>P</i> < 0.05), Moreover, the highest antibacterial and antifungal activity was found against <i>Yersinia enterocolitica</i> 33114 and <i>Saprolegnia parasitica </i>CBS 223.65 in both 30 and 60 mT magnetic fields. Moreover, the highest anticoagulation and antioxidant activity of PC and also glutathione peroxidase, glutathione reductase, superoxide dismutase, and catalase enzymes were observed under 60 mT magnetic fields. In conclusion, the use of magnetic fields can be a novel strategy for analyzing cyanobacterial pigments for their antibacterial, antioxidant, antifungal, and anticoagulation activities.