Purpose This study aimed to compare the diagnostic value of [Ga-68]Ga-DOTA-FGFR1 and [F-18]FDG PET/CT in the evaluation of lung cancer patients. Methods A prospective study was conducted between March 2023 and July 2023. Patients with high clinical suspicion of lung cancer were recruited. Each participant underwent PET/CT scanning using [Ga-68]Ga-DOTA-FGFR1 and [F-18]FDG within 6 days. Histopathology and clinical follow-up results serve as reference criteria for final diagnosis. We used a paired samples t-test or a Wilcoxon signed-rank test to compare the uptake of [Ga-68]Ga-DOTA-FGFR1 and [F-18]FDG. The diagnostic performance between the two tracers was compared using the McNemar chi(2) test. Results A total of 101 participants were included (mean age 63.267 +/- 9.344 [range 39-86 years]). In benign lung lesions, [Ga-68]Ga-DOTA-FGFR1 had lower TBR and SUVmax than [F-18]FDG (2.924 vs. 5.705, P < 0.001;1.395 vs. 4.014, P < 0.001). The TBR of [Ga-68]Ga-DOTA-FGFR1 in benign lymph nodes was also lower than [F-18]FDG (0.880 vs. 1.25, P < 0.001). [Ga-68]Ga-DOTA-FGFR1 had a higher diagnostic specificity for primary tumors than [F-18]FDG (52% vs. 28%, P = 0.031). The specificity, accuracy, and PPV of [Ga-68]Ga-DOTA-FGFR1 for detecting lymph node metastasis were 82.54%, 78.66%, and 53.73%, respectively, higher than that of [F-18]FDG (53.80%, P < 0.001, 63.15%, P < 0.001 and 38.35%, P = 0.003). However, its sensitivity in the diagnosis of lymph node and distant metastasis was not as good as [F-18]FDG PET/CT (P < 0.001, P = 0.016, respectively). There was a significant correlation between [Ga-68]Ga-DOTA-FGFR1 uptake and FGFR1 expression (Spearman r = 0.6901, p < 0.0001). Conclusions [Ga-68]Ga-DOTA-FGFR1 PET/CT had higher specificity than [F-18]FDG PET/CT for the detection of primary lung cancer. In addition, [Ga-68]Ga-DOTA-FGFR1 PET/CT also had higher diagnostic accuracy, specificity, and NPV for lymph node metastasis, but its diagnostic sensitivity for metastatic lesions was lower than [F-18]FDG PET/CT. Therefore, [Ga-68]Ga-DOTA-FGFR1 can be used as an effective supplement to [F-18]FDG to a certain extent.