If you do not have any freezer bags, you could also place the packages inside of an airtight freezer container. Remember, you can keep Girl Scout cookies for up to a year in the freezer. If the packages are open, it is better to eat them off as soon as possible, or store them in the freezer for up to two months. Thawing Them Out. Now, if you love to live on the wild side, you could actually just eat the Girl Scout cookies straight out of the freezer.