Homogeneous charge compression ignition (HCCI) engines have the potential to operate with low nitric oxide (NOx) and soot emissions. Diesel HCCI engines pose challenges related to too early combustion, high combustion rates and wall wetting of the fuel. Injecting diesel in pulses has been shown to improve combustion in these engines. In this work, diesel injected in five timed pulses has been investigated in a compression ignition (CI) engine operating in HCCI mode. The influence of varying the first, middle and last injection pulse durations alone, in sequence, while maintaining all the other injection pulse durations equal has been studied. In addition, the influence of the injection timing of the last injection pulse was also studied. A comparison of the results has been made with HCCI operation using diesel injection in a single pulse at an injection timing of 100° CA before top dead centre (TDC) and also with the conventional compression ignition mode of operation under similar outputs. The results show that, multiple pulse (MP) injection is better than injecting the fuel in a single pulse (SP) as it leads to lower emissions and higher thermal efficiency. This is because of better combustion phasing and higher heat release rates. © 2016 Elsevier Inc.