Spondyloenchondrodysplasia (SPENCD) is a rare autosomal recessive skeletal dysplasia caused by recessive mutations in the ACP5 gene, and it is characterized by the persistence of chondroid tissue islands within the bone. The clinical spectrum of SPENCD includes neurological involvement and immune dysfunction, such as systemic lupus erythematosus (SLE). To date, there are only 12 reported cases of SPENCD associated with SLE in the literature; however, detailed clinical follow-up data is absent for this comorbidity. This report presents clinical and laboratory data of three patients diagnosed with SPENCD-associated SLE. All three patients had short stature, arthralgia/arthritis, lupus nephritis, hypocomplementemia, and positive autoantibodies, including anti-nuclear and anti-dsDNA antibodies. Two patients exhibited class IV and one patient exhibited class V lupus nephritis. The early recognition of SPENCD is imperative, and this condition should be considered in patients with SLE, particularly in individuals with short stature and skeletal abnormalities. The cases presented here demonstrate that timely diagnosis and follow-up are key factors for the successful management of these conditions.