Recent thymic emigrants (RTEs) that fail post-positive selection maturation are also targeted by complement proteins. T cells likely acquire complement-resistance during maturation in the thymus, a complement-privileged organ. To test this, thymocytes and fresh serum were separately obtained and incubated together in vitro to assess complement deposition. Complement binding decreased with development and maturation. Complement binding decreased from the double positive (DP) thymocyte to the single positive (SP) stage, and within SP thymocytes, complement binding gradually decreased with increasing intra-thymic maturation. Binding of the central complement protein, C3, to WT immature thymocytes required the lectin but not the classical pathway. Specifically, MBL2 but not MBL1 was required, demonstrating a unique function for MBL2. Previous studies demonstrated that the loss of NKAP, a transcriptional regulator of T cell maturation, caused peripheral T cell lymphopenia and enhanced complement susceptibility. To determine whether complement causes NKAP-deficient T cell disappearance, both the lectin and classical were genetically ablated. This blocked C3 deposition on NKAP-deficient T cells but failed to restore normal cellularity, indicating that complement contributes to clearance but is not the primary cause of peripheral T cell lymphopenia. Rather, the accumulation of lipid peroxides in NKAP-deficient T cells was observed. Lipid-peroxidation is a salient feature of ferroptosis, an iron-dependent non-apoptotic cell death. Thus, WT thymocytes naturally acquire the ability to protect themselves from complement targeting by MBL2 with maturation. However, NKAP deficient immature peripheral T cells remain scarce in complement-deficient mice likely due to ferroptosis.