Macrophages (Mφ) are functionally dynamic immune cells that bridge innate and adaptive immune responses. However, the underlying epigenetic mechanisms that control the macrophage plasticity and innate immune functions are not well-elucidated. Here we performed transcriptome profiling of differentiating M1Mφ and M2Mφ and identified thousands of previously known and novel lncRNAs. We characterized three Mφ-enriched lncRNAs (LRRC75A-As1, GAPLINC and AL139099.5) with novel functions in Mφ differentiation, polarization and innate immunity. Knockdown of LRRC75A-As1, and GAPLINC downregulated Mφ differentiation markers CDw93 and CD68, and skewed macrophage polarization by decreasing M1 markers but had no significant impact on M2 markers. LRRC75A-As1, and GAPLINC RNAi in Mφ attenuated bacterial phagocytosis, antigen processing and inflammatory cytokine secretion supporting their functional role in potentiating innate immune functions. Mechanistically, lncRNA knockdown perturbed the expression of multiple cytoskeleton signaling thereby impairing Mφ migration suggesting their critical role in regulating macrophage polarity and motility. Together, our results show that Mφ acquire a unique repertoire of lncRNAs to shape differentiation, polarization and innate immune functions.