Harvesting should be done during early morning or late afternoon, when temperatures are lowest. One of the major problems with harvesting rambutan is that the ripening of the fruit is not uniform, within the same tree and even within the same cluster. A typical tree has fruit ripening continuously over a 30-50 day period. Therefore, several harvesting intervals of 2 to 7 days are common during the season. The fruit does not ripen after harvest and does not increase in palatable values. Rambutan is harvested ripe from 15-17 weeks after fruit-set.

Fruit-set is taken as the stage when the fruit are approximately 2 mm in diameter. They turn from green to yellow or red when ripe depending on the variety .

Harvesting criteria of some rambutan varieties based on fruit colour

Export markets require that rambutan be fresh, have a uniform reddish colour, weigh at least 30g, measure at least 1 inch (2.54 cm) in diameter, be firm with 18% soluble solids, and be free of insects, diseases and blemishes. The flesh ( aril ) should be thick and not have an off-flavour due to over maturity or fermentation. It should separate easily from the seed, which should be small. A section of the stem should be attached to all fruit.

Normally, the entire fruit cluster is harvested together by using a knife and basket attached to the end of a long pole. Fruit should not be allowed to simply fall to the ground. If single fruits are harvested, it is recommended that a piece of the stem remains attached to avoid damage to the rind. The bunches and individual fruit are collected and placed in the shade. In-field packing of rambutan is done on site if they are meant for the domestic market. Leaves are trimmed from the bunches and the stalks cut uniformly. The fruit are tied into bunches of 20, 50 or 100 fruits and these are called fruit bouquets. The loose fruit are called single fruit. The domestic market prefers fruit bouquets. The fruits must be handled carefully to avoid bruising and crushing, and kept dry, cool, and well-ventilated to delay spoilage.

The fruit are placed in plastic containers that have ventilation holes. These rigid containers of approximately 50 L capacity are stackable when filled and when empty they can be arranged with the bottom in contact with another bottom and so forth. The rigid container protects the fruit against injury during handling.

The tree may be once-over harvested or harvested at intervals of a few days. If once-over harvesting is practised all the fruit are harvested at one time. Once-over harvesting reduces harvesting time because there is no necessity to select fruit from the same tree for further harvesting. Selective harvesting takes a longer time but fruit that are harvested satisfy the correct maturity of harvest.

Generally, shoots that bear fruit in one year will put out new growth and will bloom and fruit the next year, so that biennial bearing is rare in the rambutan. However, yield may vary from year to year. Individual trees 8 years can yield as much as 200 kg one season but only 60 kg the next.