Chilli, or Capsicum annum, is a high value cash crop. Cultivation of chilli had been done using the conventional method and fertigation system. There are two methods of fertigation system practiced in Malaysia, which are planting chilli under rain shelters and open fertigation and planting chilli without rain shelter. All three planting systems have their own advantages and disadvantages. This study was conducted to evaluate the costs and benefits of chilli cultivation using both the fertigation system and conventional methods. Data were obtained from the pilot project plot under MARDI and the Department of Agriculture. The cost-benefit analysis showed that the costs of production for chilli using both fertigation systems were RM1.19/kg (under the rain shelter) and RM1.56/kg (open fertigation), respectively, compared to RM2.03/kg using the conventional method. The net income per season per hectare for planting chilli using the fertigation system under rain shelter was RM105,654 and open fertigation was RM77,415, which were higher than the conventional method (RM55,900). The higher net income was due to the high yield of chilli, almost twofold per hectare, than the conventional method. The partial budget analysis also showed a higher benefit value than the implication value in the event of farmers switching from using conventional methods to chilli cultivation using both fertigation systems. Overall, chilli cultivation using fertigation technology is proven to improve chilli yield and has a high viability. The high cost or initial capital will be offset by the high production yield. This technology is also more environmentally friendly than the conventional methods and in accordance with the practice of sustainable agriculture development, besides conforming to the present national agriculture agenda.