I didn't know you can use iterative forms that way in Czech. We use them completely different in Polish…
Would "I thought that" be "Jsem to myslila"? Is it the "va" that indicates the imperfect tense in Czech? Děkuji vam!
Jsem should go in the second position and the verb is reflexive "myslet si".
So: Myslela jsem si to.
And as iyoossaev points out, the verb is imperfective. In fact the original myslet si is imperfective as well. The -va- gives it the "used to" meaning. It can be mostly only used in the past. As discussed in older comments, this is an iterative form, it expresses habitual repeating of the action.