Objectives We sought to investigate the sex distribution, clinical presentations, disease outcomes and genetic background of early-onset paediatric systemic lupus erythematosus (eo-pSLE) in a single centre in China to help enable early diagnosis and timely treatment. Methods The clinical data of children aged less than five years with SLE (n = 19) from January 2012 to December 2021 were reviewed and analysed. We performed DNA sequencing in 11 out of 19 patients to survey the genetic etiologies. Results Our study included 6 males and 13 females. The mean age at onset was 3.73 years. The median diagnostic delay was 9 months and was longer in male patients (p = 0.02). Four patients had an SLE-relevant family history. The most common clinical manifestations at diagnosis were fever, rash, and hepatosplenomegaly. ANA positivity and low C3 were identified in all children. The renal (94.74%), mucocutaneous (94.74%), haematological (89.47%), respiratory (89.47%), digestive (84.21%), cardiovascular (57.89%), and neuropsychiatric (52.63%) systems were involved to varying degrees. We identified 13 SLE-associated gene mutations in 9 out of 11 patients: TREX1, PIK3CD, LRBA, KRAS, STAT4, C3, ITGAM, CYBB, TLR5, RIPK1, BACH2, CFHR5, and SYK. One male patient showed a 47, XXY chromosomal abnormality. Conclusion Early-onset (<5 years) pSLE is characterized by an insidious onset, typical immunological patterns, and the involvement of multiple organs. Immunological screening and genetic testing should be performed as soon as feasible in patients with an early onset of multisystemic autoimmune diseases to confirm the diagnosis.