A positron emission tomography (PET) scanner using a silicon photomultiplier (SiPM PET) in place of a photomultiplier tube significantly improves the spatial and time resolution. It may also improve the evaluation of smaller lesions compared to conventional (non-SiPM) PET scanners. We compared the maximum standardized uptake value (SUVmax), detection sensitivity, and morphological correlation using magnetic resonance imaging (MRI) for primary tongue squamous cell carcinoma between the SiPM PET and non-SiPM PET scanner. We retrospectively reviewed the F-18 fluorodeoxyglucose (FDG) PET/CT features of tongue squamous cell carcinomas in consecutive, newly diagnosed, and pathologically verified patients. Twenty-five of 46 patients were scanned using SiPM PET scanner and the remaining 21 patients were scanned with a non-SiPM PET scanner. We compared the SUVmax and visual evaluation of primary tumor detectability, and the correlation between the PET-based and MRI-based tumor size (long axis, thickness, and volume). Differences in SUVmax and detection sensitivity for the primary tumor were analyzed using Welch's t test and Fisher's exact test, respectively. Correlations among the PET-based, MRI-based tumor size, and SUVmax were assessed using Spearman's rank correlation coefficient. SUVmax of both T1/T2 and T3/T4 primary tumors were significantly higher for the SiPM PET (T1/T2 mean SUVmax: 6.6 ± 4.3, T3/T4 mean SUVmax: 18.2 ± 9.8) than that for the non-SiPM PET (T1/T2 mean SUVmax: 3.4 ± 1.4, T3/T4 mean SUVmax: 10.2 ± 4.9) (P < 0.05). While all cases of T3/T4 primary tumors were detected by both PET scanners, the detection sensitivity for T1/T2 primary tumors was significantly higher for the SiPM PET (80%) than that for the non-SiPM PET (36.4%) (P < 0.05). MRI-based tumor size correlated significantly with SiPM PET-based tumor long axis (ρ = 0.74) and volume (ρ = 0.91), but not with the non-SiPM PET-based tumor long axis and volume in T1/T2 primary lesions. Correlation between MRI-based tumor size and SUVmax was significant in both PET scanners; however, no significant difference was observed between the two scanners. The SiPM PET provides better detection sensitivity and a reliable morphological correlation for the T1/T2 primary tongue tumors than the non-SiPM PET due to its high performance.