My pup was recently vaccinated and has a lump in the middle of his neck, will it go away?

Hi Goureme,
If it is simply accumulated fluid do to the injection, it will eventually absorb into his system. As long as it has not appeared later on, resultant from an infection or some such cause, you should have nothing to worry about.
There are some knowledgeable people here who can perhaps give you a better answer later on.
Sorry I can't be of more help. Take care.

It is not uncommon for a dog to get a knot at the injection site several days to weeks after vaccination. It can last for several months. However, if it continues to grow, cause pain, or erupt please contact your vet ASAP!