Background: An inverse relationship of serum liver transaminases and mortality might be due to better blood pressure control in hypertensive patients. Whether it holds true regarding such an association for long-term blood pressure variability (BPV) in those without antihypertensive therapy is unclear. Methods: A population of 1112 military males without antihypertensive medications, aged 32 years, was collected from a retrospective longitudinal study in Taiwan. Serum liver aspartate and alanine transaminase (AST and ALT) levels were obtained from a 12 h-fast blood sample of each participant. BPV was assessed by standard deviation (SD) and average real variability (ARV) of systolic and diastolic blood pressure (SBP and DBP), respectively across 4 visits during the study period (2012–2014, 2014–2015, 2015–2016, and 2016–2018). Multivariable linear regression analysis was utilized to determine the association adjusting for demographics, anthropometric indexes, SBP, DBP, and lipid profiles. Results: In the unadjusted model, ALT was significantly and positively correlated with SDDBP and ARVDBP (β (standard errors) = 0.36 (0.16) and 0.24 (0.12), respectively), and so was AST (β = 0.19 (0.08) and 0.14 (0.06), respectively). All the associations were insignificant with adjustments. However, ALT was significantly and negatively correlated with SDSBP and ARVSBP (β = −0.35 (0.14) and −0.25 (0.11), respectively) and so was AST (β = −0.14 (0.07) and −0.12 (0.06), respectively) with adjustments. Conclusion: Our findings suggested that serum liver transaminases were negatively correlated with long-term systolic BPV in young male adults without antihypertensive therapy, and the clinical relevance needs further investigations.