Epithelial ovarian cancer (EOC) is one of the most malignant gynecological tumors worldwide. Deregulation of long non-coding RNAs (lncRNAs) has been implicated in various oncogenic processes in multiple cancers. In this study, we aim to identify and characterize clinically relevant lncRNA deregulation in EOC. LncRNAs, mRNAs and miRNAs were profiled using expression microarrays and validated using reverse transcription quantitative PCR in EOC cells and tissues. siRNAs targeting either HOXD-AS1 or PIK3R3 together with miR-186-5p inhibitors were used to modulate endogenous target expression in EOC cell lines in vitro. In vitro wound healing assay, trans-well assay, Western-blot assay,and Dual-luciferase reporter assay were used to explore the biological roles and molecular function underlying HOXD-AS1 in the EOC cells. Progression-free survival (PFS) and overall survival (OS) were statistically analyzed by Kaplan-Meier method test. HOXD-AS1 was found to be significantly over-expressed in EOC tumors. High HOXD-AS1 expression significantly correlated with poorer PFS and OS of EOC patients. Multivariate Cox proportional hazards modeling indicated that HOXD-AS1 was an independent risk predictor of EOC patients (HR = 1.92, p = 0.004). SiRNA inhibition of HOXD-AS1 reduced cell migration, invasion, and epithelial-mesenchymal transition (EMT) in EOC cells in vitro by preventing HOXD-AS1 directly binding to miR-186-5p, and resulting in down-regulating of PIK3R3. The novel HOXD-AS1/miR-186-5p/PIK3R3 pathway was clinically relevant as we observed a significantly inverse correlation between HOXD-AS1/miR-186-5p and between miR-186-5p/PIK3R3 in an independent cohort of 200 EOC tissues. HOXD-AS1/miR-186-5p/PIK3R3 is a novel pathway to promote cell migration, invasion, and EMT in EOC.