Apple fruits experience a variety of conditions in the supply chain which causes mechanical damages, scaring, and bruising and ultimately reduce the quality and shelf life of the product. Studies were carried out for two consecutive years (2013 and 2014) to identify the appropriate packaging method for minimization of transportation loss. Different Packaging methods were evaluated for assessing damage that occurs during transport. Red Delicious apple fruits harvested on 3rd week of September from HRS, Jumla, Nepal were transported to Kohalpur, Banke, Nepal (215 km mountainous gravel road, 48 hours) in 5 Ply 160 PSI bursting strength CFB boxes with the following treatments; fruits with full stalk and with trimmed stalk, separated inside CFB boxes with deck plate and all together, individual fruits wrapped with styrofoam and no wrapping, and with 8 ventilation hole in CFB box and without ventilation hole. The CFB boxes were sealed and loaded randomly; stacked in 4 layers inside the truck after spreading of HDPE tarpaulin at the base and shipped to Kohalpur, Banke, Nepal. To find out the effect of packaging method as it may not be apparent immediately the fruits were stored at 5±1℃ and 95% RH for one month. After storage, observations were made on physiological loss in weight (PLW), total damage, acceptable and unacceptable damage, fruit quality and economic analysis. The result revealed that all the treatments imposed reduced PLW; percent damaged fruits and maintained better quality. Among different treatment combinations, wrapping of stalk trimmed individual fruits in ventilated CFB box separated in layers with deck plate was found the best method. Damaged fruits were reduced to 3.8% as compared to 18.2% in ordinary packaging.