Long noncoding RNAs (lncRNAs) play important roles in the regulation of immunological and apoptotic function. Here, we aimed to explore critical immune- and apoptosis-related lncRNAs in the occurrence and development of Henoch-Schönlein purpura nephritis (HSPN) in children. Through differentially expressed analysis, we identified differentially expressed lncRNAs, immune- and apoptosis-related mRNAs in the peripheral blood samples of children with HSPN. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses validated the immunological and apoptotic roles of the differentially expressed immune-related and apoptosis-related mRNAs. Following, we analyzed the correlations of differentially expressed lncRNAs and immune- and apoptosis-related mRNAs by Spearman’s correlation analysis, and determined 100 critical immune- and apoptosis-related lncRNAs in HSPN of children. Based on competing endogenous RNAs (ceRNA) mechanism, we constructed the immune- and apoptosis-related lncRNA-miRNA-mRNA regulatory network in HSPN of children, and validated the expression levels of lncRNAs in the lncRNA-miRNA-mRNA regulatory network. Collectively, we proposed that the immune- and apoptosis-related lncRNA-miRNA-mRNA regulatory network might participate in the modulation of pathogenesis of HSPN in children. In addition, the lncRNAs in the immune- and apoptosis-related lncRNA-miRNA-mRNA regulatory network (upregulated SNHG3, LINC00152, TUG1, GAS5, FGD5-AS1, DLEU2, and SCARNA9; downregulated SNHG1, NEAT1, DISC1-IT1, and PVT1) could become novel biomarkers for the diagnosis of HNSP in children.