Agroforestry (AF), a traditional land management system in Pakistan that provides great potential both to boost agriculture and reduce wood shortages. Previous work has identified many complex factors of AF covering socio-economic, and environmental impacts. Comparatively few have addressed the perception of the impact of AF. This study investigates the farmer perception of ecological impact derived from AF and the factors that influence their perception. The questionnaire was completed by 200 farmers in Northern irrigated plain in Pakistan, and the resulting descriptive statistics and a probit regression analysis were used to analyze the data. The results show that majority of farmers were believed AF increases the greenery, understory regeneration, water retention, and soil fertility of the farmland. In addition, the analysis shows that farmers’ perceptions of AF were positively correlated with the native trees selected for cultivation. However, farmers who practice agrosilvopastoral system had less knowledge and perception of the ecological benefits of AF. Moreover, the study found, even though farmers plant exotic species they perceived that it had a negative impact on the water level and soil fertility. On the other hand, lack of technical knowledge also affected their perceived status. Therefore, designing and implementing informal education programs that collaborate with AF farmers and officials is suggested.