We have had SO much trouble with MTX with my daughter, which is a shame, because it worked like a miracle for my daughter's arthritis.
So, here are our tricks:
1) Shot over pills - M had a very hard time with the pills - nausea, mouth ulcers. The shot definitely had fewer side effects and it's a tiny, tiny needle and a pretty painless shot - she gave it to herself even when she was 13-14 years old.
2) Zofran -Before we gave M the MTX at night, we gave her Zofran. Then gave Zofran again in the morning. Zofran made her tired but helped with the nausea and dizziness. We found that the dissolvable Zofran worked faster than the regular pills.
3) Folic acid - M took 2mg per day - increasing the dose meant no more mouth ulcers, though M did still have nausea/dizziness.
4) Leucovorin - For whatever reason, rheumatologists seem to prescribe this more than GI's. It is folinic acid - a "rescue drug" used with MTX, typically when MTX is used in high doses for cancer. The doses used for IBD of both Leucovorin and of MTX are much lower. The Leucovorin REALLY helped my daughter with the side effects of MTX. She took it the morning after MTX, I believe.
5) Nausea drugs - Besides Zofran, the other drug we had success with is Kytril (Granisetron). M's rheumatologist prescribed it - it's very similar to Zofran, but seemed to work better for M. It's used a lot with chemotherapy. Insurance does not like it because it's expensive but did pay for it. The last time M was on MTX (she's been on MTX three separate times) we used it instead of Zofran.
Unfortunately, M just could not deal with MTX, as I said, we tried it 3 different times at 3 different doses (25mg, 15mg and 7.5mg - by injection). She had an extreme reaction - she would be so nauseous and dizzy that she was in bed for two days a week and it just wasn't worth it. Decreasing the dose helped but just not enough to make it worth dealing with every week.
Most kids have mild side effects though, that can be managed. M's older sister takes MTX with just some nausea and tiredness the day after the shot - no real issues.