Heavy metals contaminate soil and adversely affect plant growth. These soils contain different fungi and bacteria which exhibit metal tolerance and work as bioremediation agents to detoxify polluted soils. In the present study, polluted soil samples were collected to estimate the contamination of copper (Cu) and cadmium (Cd). From this contaminated soil, metal tolerant fungi were isolated and characterized. Copper and cadmium were found in a range of 190.2–300.4 mg/kg and 46.8–56.1 mg/kg, respectively. For the isolation of metal tolerant fungi, soil dilutions were made in water and inoculated on potato dextrose agar (PDA) media. Fungal growth was observed on PDA and successive screening resulted in the isolation of four multi-metal tolerant fungal species, including Penicillim oxalicum, Fusarium solani, Aspergillus niger and Trichoderma harzianum. Sequencing of 18S rRNA genes of isolated fungi also efficiently identified them. To reveal minimum inhibitory concentrations (MIC), these fungi were exposed to increasing concentrations of cadmium and copper chlorides (100 to 1000 ppm) and a variable MIC range of 400 ppm to 1000 ppm was estimated. Based on tolerance index analysis, F. solani was found to be resistant at 1 mM copper, while P. oxalicum was the most tolerant species under cadmium stress. F. solani and P. oxalicum demonstrated the highest biosorption capacity of Cu and Cd, respectively. Both metals negatively affected wheat seedlings in a pot experiment, while the treatment of both F. solani and P. oxalicum positively influenced the germination and growth of wheat. Based on these observations, it could be inferred that F. solani and P. oxalicum can be used for the myco-remediation of Cu and Cd, respectively.