Setaria digitata is a Wolbachia-free filarial parasite that causes cerebrospinal nematodiasis in non-permissive hosts such as goats, sheep and horses leading to substantial economic losses in animal husbandry. Due to its similarity to Wuchereria bancrofti, primary causing agent of human lymphatic filariasis (HLF), S. digitata can be used as a model organism to study the biology of HLF. This study was mainly aimed to bring functional analysis of metabolic pathways in S. digitata. A draft genome of 78,774,594 bases making a total of 2,075 contigs was generated. ‘BLAST2GO’ functional annotation resulted in 28112 BLAST hits with an e-value lower than 1e-4 and a sequence similarity higher than 30%. Out of a total of 2075 contigs, 1280 contigs were used to generate a total of 6055 GO annotations at a mean level of 6.488 with standard deviation of 2.675. Overall, 89.1% of mapped reads were annotated by at least one of the three categories of the GO function classification. Moreover, 111 enzymes associated with 95 distinct metabolic pathways were identified. We suggest that S. digitata may have evolved its own sequences to code for haem, riboflavin, and FAD in the absence of Wolbachia.