When transporting guinea pigs, it is very important to consider their exceptionally shy nature. The transporting process will usually be a very stressful time for the guinea pigs and so care must be taken to minimize stress as much as possible. Guinea pigs will commonly freeze when being transported but will usually recover within an hour if left undisturbed. Provision should always be made for somewhere for them to hide during transport. Stress will arise from catching, being in unfamiliar surroundings, deprivation of food and water and noise and changes in temperature.

Food and water should never be withheld from guinea pigs for more than a few hours. Guinea pigs have strict eating routines that they follow every day, always eating at around the same time. If food and water is withheld from a guinea pig during this period, they will become very stressed. For short trips to the vet or to shows, avoid transporting guinea pigs during their usual feeding times. On longer trips, provide hay and fresh vegetables as a source of moisture, and offer them water throughout the trip.

Appropriate travel cages must be used for transporting guinea pigs to ensure their safety and to reduce their level of stress. A fully enclosed plastic carry case for rabbits, cats and other small animals should be used. Solid walls ensure that the interior is kept dark, which will reduce stress, and a towel or sheet over the doorway of the cage will minimize light. However, take care to ensure that the cage is still well-ventilated and that the guinea pigs have access to fresh air. Line the inside of the cage with a thick layer of newspaper and place a large handful of hay (approximately one third of cage size) in the cage. This provides the guinea pigs with nesting material that they can hide away into for comfort. While guinea pigs will not chew through cardboard or cloth like rats and mice, it is not recommended to transport them in cloth or cardboard crates as these are not as secure and will not provide as much safety during transport. Two guinea pigs can be transported together however more than 2 animals should never be transported together as trampling can occur. Always keep the cage upright and ensure that it is secured to prevent tipping and movement in the vehicle. Guinea pigs must be transported inside an enclosed vehicle.

It is a good idea to quarantine new guinea pigs from existing guinea pigs for a period of time. This should allow time for observation of any signs of illness or parasite infestations.