The tasks to improve diesel emissions and fuel consumption must be accomplished with urgency. However, due to the trade-off relationship between NOx emissions, soot emissions and fuel consumption, clean diesel combustion should be achieved by both innovative combustion and fuel technologies. The objective of this study is to extend the clean diesel combustion operating range (Engine-out emission: NOx ≺ 0.2 g/kWh, Soot ≺ 0.02 g/kWh). In this study, performance of a single-cylinder test engine equipped with a hydraulic valve actuation system and an ultra-high pressure fuel injection system was investigated. Also evaluated, were the effects of fuel properties such as auto-ignitability, volatility and aromatic hydrocarbon components, on combustion performance. The results show that applying a high EGR (Exhaust gas recirculation) rate can significantly reduce NOx emission with an increase in soot emission. However, using a low cetane number fuel could suppress soot emission because it can prolong premixing periods of fuel and in-cylinder gas. Additionally, a high volatility fuel could decrease soot emission because it promotes evaporation of fuel and mixing with in-cylinder gas. Cetane number and aromatic hydrocarbon components also affect combustion performance when combined with the hydraulic valve actuation system and the ultra-high pressure fuel injection system. It is concluded that an optimal fuel for an advanced diesel engine has lower cetane number (CN: 40~45) and no aromatic hydrocarbon. Furthermore, the testing verified that a combination of ultra-high pressure fuel injection and high pressure turbo-charging could expand operating ranges for ultra clean and silent combustion.