The increasing demand for sustainable agricultural practices has led to growing interest in evaluating the environmental impacts of hydroponic systems. This study assesses and compares the carbon footprint of hydroponic Sweet Hami melon cultivation in two commercial greenhouse systems in the Special Region of Yogyakarta, Indonesia, using a life cycle assessment (LCA) approach following ISO 14067 standards. The system boundary was defined as cradle-to-farm gate, and the functional unit was 1 kg of fresh melon. Primary data were collected from two greenhouse farms, D’Pands Agrofarm and Wanadelima Orchard, covering one full cultivation cycle (October 2024 to January 2025). Life cycle inventory (LCI) data included electricity, water, fertilizers, and material inputs, while background processes were obtained from the Agribalyse 3.0 database. The impact assessment was conducted using the IPCC GWP100 method. Uncertainty analysis was performed using Monte Carlo simulation with 1,000 iterations. The results show that D’Pands Agrofarm has a higher carbon footprint (1.619 kg CO₂-eq per kg of melon) compared to Wanadelima Orchard (1.238 kg CO₂-eq per kg of melon). Electricity consumption was identified as the dominant contributor, followed by fertilizer inputs. Contribution analysis indicates that differences in resource use, particularly energy demand and water treatment efficiency, significantly influence total emissions. Monte Carlo simulation supports the reliability of the results and confirms a clear distinction between the two systems. This study provides empirical evidence from tropical hydroponic greenhouse systems and demonstrates that variations in structural and operational characteristics significantly influence carbon footprint outcomes. The findings suggest that improving energy efficiency and optimizing resource management are key strategies for reducing environmental impacts in hydroponic cultivation systems.