If he carries a smart phone or tablet, that makes a fine place to install the Micro SD when it's not being used to transfer data to or from the school.
He's a good bit less likely to lose such a device than something smaller than a postage stamp, and he can actually use (some of) the information on the Micro SD while he's carrying it (say, on a school bus).
lifehacks.stackexchange.com/users/9830/Zeiss Ikon
Use a case which is big enough not to get lost.
You can get small cases which are pretty much waterproof and you can often put a keyring through the case, so you can attach it to the lanyard.
I googled SD card case, and found a lot of pictures, (but all on commercial sites.)
lifehacks.stackexchange.com/users/19058/Willeke
Not a lifehack as such, but they do sell cases for sd cards which attach to your key ring or lanyards.
This will both protect the sd card, and if keys are attached make it easier to keep track of.
Edit:
We're not supposed to advertise specific cases, but here is a Google search returning multiple cases: micro sd keychain case
lifehacks.stackexchange.com/users/4490/holroy
A case for the sd card could solve the problem (as Willeke suggested), but would require keeping track of it while using the sd card and putting the card back in each time.
Keeping
it permanently plugged into the computer
could work (as Zeiss Ikon suggested), but would require the laptop to have the proper port, and may fall out.
Now for my solution, use a device like this (not necessary the same brand): A small rubber band tightly wrapped around could help hold the card.
It is not very clear from the image, but it has a loop in the end to which a string can be attached.
The device is called a "USB 2.0 SD/MMC Memory Card Reader", and the web page
I found it on is http://www.bestbuy.com/site/insignia-usb-2-0-sd-mmc-memory-card-reader-black/3602009.p?skuId=3602009
lifehacks.stackexchange.com/users/9624/k-l
If you have any contact lens case you can use that or I used to carry my sd card into an empty vapor-rub case as shown below.
lifehacks.stackexchange.com/users/20463/Amit Bisht
My son will be required to carry a micro SD card back and forth to ninth grade next year.  What can we put it in so it doesn't get lost or damaged?  (Extra challenge: He has ADHD.)  For a flash drive, we bought one with a little hole on one end.  We put a simple, sturdy key ring through the hole, and attached it to a lanyard.  That worked well.
How to carry *one* SD card in a crowded knapsack without losing it?
lifehacks.stackexchange.com
<organization>
lifehacks.stackexchange.com/questions/15583
lifehacks.stackexchange.com/users/5433/aparente001
The best way to avoid losing an SD card in a crowded knapsack is probably to keep it inside something else which is bigger, such as a smart phone or tablet. Alternatively, you could buy a waterproof case with a keyring attached. The options are to install the Micro SD in a smart phone or tablet or to use a case that is big enough not to get lost, for example a contact lens case.
Install the SD in a smart phone or tablet. Use a case that is big enough not to get lost - there are plenty on the market. Use a case for the sd card and wrap a rubber band around it to help hold the card. Use a contact lens case.