Learning words in Japanese could mean:

1. learning the sounds and the meaning (using a phonetic script, such as hiragana or romaji - the Latin alphabet) or

2. Learning sound, meaning and kanji (the ideograms)

Learning the kanji is a topic in itself and there are dozens of methods and approaches, but if you like the "start with the most valuable first then build on top of that one bit of knowledge at a time" approach, you might be interested in a project I worked on a while ago: https://prezi.com/m/ihobq38emnq3/env3/

I have flashcards with example sentences up to the first 300 items or so, contact me if you're interested.