The management of pest insects is the critical component of agricultural production especially in the fertigation based farm. Although the fertigation farm in Malaysia has advantages in the fertilization and irrigation management system, it still lacking with the pest management system. Since almost the insect and pests are living under the crop's leaves, it is difficult and hard labor work to spray under the leaves of the crop. Almost agricultural plants are damaged, weakened, or killed by insect pests especially. These results in reduced yields, lowered quality, and damaged plants or plant products that cannot be sold. Even after harvest, insects continue their damage in stored or processed products. Therefore, the aim of this study is to design and develop an autonomous pesticide sprayer for the chili fertigation system. Then, this study intends to implement a flexible sprayer arm to spray the pesticide under the crop's leaves, respectively. This study involves the development of unmanned pesticide sprayer that can be mobilized autonomously. It is because the pesticide is a hazardous component that can be affected human health in the future if it exposed during manual spraying method especially in a closed area such as in the greenhouse. The flexible sprayer boom also can be flexibly controlled in the greenhouse and outdoor environment such as open space farms. It is expected to have a successful pesticide management system in the fertigation based farm by using the autonomous pesticide sprayer robot. Besides, the proposed autonomous pesticide sprayer also can be used for various types of crops such as rockmelon, tomato, papaya. pineapples, vegetables and etc.