Filamentous fungi are versatile microorganisms vital in the industrial production of organic compounds and enzymes. They are crucial for various other ecosystems due to their ability to form symbiotic relationships and thrive in various environments. Their beneficial properties, such as the ability to cultivate in inexpensive media, high secretion, and efficient eukaryotic-like post-translational modification and protein folding, make the fungal-based protein production system superior to the bacterial-based system. The dearth in understanding of the secretory pathways and physiology of fungi in depth has stalled the accelerated modification of strains to produce heterologous proteins. This chapter highlights the various filamentous fungal species in use, including Aspergillus, Trichoderma, Penicillium, and Myceliophthora, for the production of heterologous protein. Various techniques used in the enhancement of the fungal strains for efficient heterologous production, such as the regulation of protein folding, codon optimization, carrier protein fusion, glycosylation engineering, selection of promoters, signal peptides, and development of a protease-deficient strain, have also been discussed briefly. Insights on various filamentous fungi used for industrial heterologous protein production, and various examples of proteins produced, are also included. Despite bottlenecks in the expression and production of protein, filamentous fungi are a critical force in the field of biotechnology and molecular biology. Hence, a deeper understanding of secretory pathways will enhance the utilization of filamentous fungi.