Background: Ziarat juniper (Juniperus excelsa M.Bieb) is an evergreen and dominant species of Balochistan juniper forests. This forest is providing many benefits to regional ecosystems and surrounding populations. No functional genomics study is reported for this important juniper plant. This research is aimed to characterize the Ziarat juniper functional genome based on the analyses of 1500 transcripts. Methods: Total RNA from shoot of Juniperus excelsa was extracted and subjected for transcriptome sequencing using Illumina HiSeq 2000 with the service from Macrogen, Inc., South Korea. The Illumina sequenced data was subjected to bioinformatics analysis. Quality assessment and data filtration was performed for the removal of low-quality reads, ambiguous reads and adaptor sequences. The high-quality clean reads data was deposited in the Sequence Read Archive (SRA) at NCBI, and used for downstream processes. Fifteen hundred transcripts were randomly chosen and used for functional characterization. Results: As a result of homology search 80.3% transcripts showed significant similarities and were placed in significant similarities category, 19.3% transcripts showed low similarities and assigned to the ‘‘unclassified’’ category while 0.4% transcripts are defined as no hits. The functional characterization results showed that most (18%) of the transcripts are involved in metabolism, followed by 11.7% in transcription and 11.5% as structural protein. 8.8% transcripts are engaged in stress response, whereas the transcripts involved in growth and development constituted 6.7%. Transcripts involved in signal transduction represented 5.6%, while 3.5% facilitating transport and 34.1% are involved in hypothetical functions. Conclusion: The functional annotation data produced in this study will be very useful for future functional genome analysis of Juniperus excelsa.