The eggplant fruit and shoot borer (Leucinodes orbonalis Guenée) is a devastating lepidopteran pest of the eggplant (Solanum melongena L.), causing significant economic losses. Reference genomes aid in understanding insect pest biology and can guide pest management programs. For eggplant fruit and shoot borer, however, genomic resources are scarce; hence, this study presents an annotated genome assembly of the Philippine eggplant fruit and shoot borer genome using Illumina short reads. The 480,399,388 bp long assembly contained 31,568 contigs with an N50 of 204,698 bp and a BUSCO score of 96.5%. Annotation of repeat elements indicates that the eggplant fruit and shoot borer genome comprises 38.50% interspersed repeats, which are mostly unclassified repeats. Functional RNA annotation revealed 1,310 functional RNA genes consisting primarily of tRNAs, rRNAs, snRNAs, and miRNAs. Protein structural annotation predicted a total of 12,671 genes. Annotation using a Cluster of Orthologous groups indicates proteins belonging to group S (unknown), group T (signal transduction), group O (posttranslational modification), and group K (transcription). Of the proteins belonging to group S, PFAM analysis revealed proteins containing chitin, juvenile hormone, odorant and pheromone-binding protein domains, and zinc finger motifs. Further analysis of the predicted proteins indicates that the EFSB possesses conserved biochemical machineries in insect chemosensation, detoxification, and hormone biosynthesis and reception. Variation profiling, on the other hand, detected 11,103,848 SNPs and 3,031,155 indels possibly occurring in Philippine eggplant fruit and shoot borer. Overall, the genome assembly and annotation generated from this study contribute to establishing genome references, and may aid in understanding the EFSB through future studies aimed at its effective control.