Long noncoding RNA (lncRNA)-mediated epigenetic regulation plays important roles in wide range of biological processes and diseases. Here, we applied comprehensive analyses of RNA-seq and CAGE-seq (cap analysis of gene expression and sequencing) to characterize the dynamic changes in lncRNA expression in rhesus macaque brain in four age groups from postnatal to aged periods. We identified 18 anatomically diverse lncRNA modules and 14 mRNA modules representing spatial, age and sex specificities.Spatiotemporal- and sex-biased changes in lncRNA expression are in general higher than that observed in mRNA expression. A negative correlation between lncRNA and mRNA expression in cerebral cortex was observed, such relationship was further explored and functionally validated. Our findings offer an initial insight into spatial-, age- and sex-biased changes in lncRNA expression inmacaque brain, and that the distinct classification of such changes might represent a previously unappreciated regulatory system which potentially contributes to brain development and ageing.