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The aim of this study was to identify differentially expressed lncRNAs (DElncRNAs) and mRNAs (DEmRNAs) in the endometrium of individuals with and without endometriosis (EMS) during the proliferative (P) and secretory (S) phases of the menstrual cycle. Tissues were obtained from 18 control (CT; P-phase [pCT], <i>n</i> = 8; S-phase [sCT], <i>n</i> = 13) and 23 EMS patients (P-phase [pEMS], <i>n</i> = 13; S-phase [sEMS], <i>n</i> = 12). DElncRNAs and DEmRNAs were analyzed using total RNA-sequencing. In P-phase, expression of <i>NONHSAG019742.2</i> and <i>NONHSAT120701.2</i> was significantly higher in EMS than control patients, that of while <i>NONHSAG048398.2</i> and <i>NONHSAG016560.2</i> was lower in EMS patients. In S-phase, expression of <i>NONHSAT000959.2</i>, <i>NONHSAT203423.1</i>, and <i>NONHSAG053769.2</i> was significantly increased in EMS patients, while that of <i>NONHSAG012105.2</i> and <i>NONHSAG020839.2</i> was lower. In addition, the expression of <i>HSD11B2</i>, <i>THBS1</i>, <i>GPX3</i>, and <i>SHISA6</i> was similar to that of neighboring lncRNAs in both P- and S-phases. In contrast, <i>ELP3</i> and <i>NR4A1</i>, respectively, were up- or downregulated in pEMS tissues. In sEMS, expression of <i>LAMB3</i> and <i>HIF1A</i> was increased, while expression of <i>PAM</i> was reduced. Our findings on lncRNAs and mRNAs encourage not only exploration of the potential clinical applications of lncRNAs and mRNAs as prognostic or diagnostic biomarkers for EMS but also to gain valuable insights into its pathogenesis.