Objective Long noncoding RNAs (lncRNAs) are reported to play crucial roles in several physiological and biological processes. However, knowledge of lncRNAs in children with systemic lupus erythematosus (cSLE) remains limited. We investigate lncRNA expression profiling of cSLE and explore the potential function of lncRNAs. Methods LncRNA and mRNA microarrays were performed to identify changes in lncRNA and mRNA expression between children with SLE and paired healthy children. Quantitative polymerase chain reaction (qPCR) validated these results. A Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed to explore the potential lncRNA function. Results A comparison between children with SLE and paired healthy children revealed that 1042 lncRNAs and 1162 mRNAs were differentially expressed. By using gene co-expression network analysis, we constructed a complex lncRNA target network consisting of 817 matched lncRNA-mRNA pairs for 309 differentially expressed lncRNAs and 210 differentially expressed mRNAs. The results of further GO and KEGG pathway analyses indicated that lncRNAs were involved mainly in pathways with crucial pathobiological relevance in SLE. Conclusion We firstly characterised the expression prbfiles of lncRNA and mRNA in children with SLE and propose herein their possible roles in the pathogenesis of SLE. These results provide novel insights into the mechanisms of SLE pathogenesis and may serve as diagnostic biomarkers for SLE therapy.