Background: AXL, a tyrosine kinase receptor, is involved in epithelial-to-mesenchymal transition (EMT), cell survival, invasion, metastasis, and resistance to EGFR-TKIs and immune checkpoint inhibitors (ICIs). Recent clinical studies have shown promising results in NSCLC patients treated with AXL inhibitors. Methods: We evaluated AXL-mRNA overexpression in CTC fractions of NSCLC patients under osimertinib treatment (Group A, n = 39), (collected in the context of a multicenter Phase II clinical study (ClinicalTrials.gov number: NCT02771314) or immunotherapy (Group B, n = 116) at different time points collected in the context of a prospective, multicenter study (ClinicalTrials.gov number: NCT04490564). Size-based CTC enrichment (Parsortix, CelLBx Health, Guildford, UK) was used, and AXL-mRNA overexpression was evaluated using RT-qPCR. Results: In Group A, AXL-mRNA overexpression in CTC fractions was detected in 5/39 (12.8%) patients’ samples at baseline, in 5/31 (16.1%) after one cycle of treatment, in 7/79 (8.9%) during treatment and in 4/32 (12.5%) at progression of disease (PD). In Group B, AXL-mRNA overexpression in CTC fractions was detected in 8/116 (6.9%) samples before immunotherapy, in 8/71 (11.3%) after three or four cycles, while no AXL transcripts were detected at PD. Conclusions: Our results indicate that AXL-mRNA overexpression in CTC fractions deserve to be further evaluated through larger clinical studies as a potential biomarker for anti-AXL targeted therapies in NSCLC.