Fast and accurate methods of immature citrus fruit detection are critical to building early yield mapping systems. Previously, machine vision methods based on color images were used in many studies for citrus fruit detection. Despite the high resolutions of most color images, problems such as the color similarity between fruit and leaves, and various illumination conditions prevented those studies from achieving high accuracies. This project explored a novel method for immature citrus fruit detection by using videos from a thermal camera, which can capture the surface temperatures of citrus canopies. Fruit and leaves in citrus canopies have different thermal characteristics, which can present different temperatures during a heating or a cooling process. An active thermography system was developed which created a thermal excitation signal on the surface of citrus canopies to change their temperatures and then take thermal images. Because of the high temperatures in Florida during the growth period of citrus fruit, a cooling method was selected by spraying water. The system was implemented using a golf cart, on which a water spray system and a thermal imaging system were mounted. The water spray system installed in the front of the golf cart sprayed water on the surface of citrus canopies. Then the thermal imaging system, which was mounted at the end of the golf cart, acquired videos of the citrus canopies. Novel fruit detection and tracking algorithms were developed for counting the number of fruit from the videos. An average precision of 87.2% was achieved using thermal video frames for immature citrus fruit detection.