First, let's start with the word "a wish" - which is משאלה in Hebrew - from your well-known root ש.א.ל. - same as in the word "question" שאלה or "to ask" - לשאול.

But what do we do with the wish? First, we - as you are probably expecting already, we don't have the expression "come true." Is there another way to say it in English that would help us? Yes, there is - one can "grant" a wish or "fulfill" a wish. And that works in Hebrew! Just in a shorter version - for us "fulfill" is same as "fill" - למלא.

So - "to make a wish come true" = "to fulfill a wish" - למלא משאלה.

Examples:
⮞ In fairy tales they tell that a goldfish can grant three wishes.
באגדות עם מספרים שדג זהב יכול למלא שלוש משאלות. (audio #1)
⮞ Every parent knows that if one grants every wish of a child and never say "no" he will grow up spoiled.
כל הורה יודע שאם ממלאים כל משאלה של הילד ואף פעם לא אומרים "לא" - הילד יגדל מפונק. (audio #2)

But there is another way to say it, actually! What else (in English) can "come true?" A dream, of course! And how would we say in Hebrew "to make a dream come true"?
That would be a different verb! להגשים חלום, we say!
Interestingly, this verb also works with the משאלה word perfectly!

Examples:
⮞ Don't give up, keep searching for ways to make your dream come true!
אל תוותר, תמשיך לחפש דרכים להגשים את החלום שלך! (audio #3)
⮞ It will help to make all you wishes true!
זה יעזור לכם להגשים את כל משאלותיכם! (audio #4)

It can be also used in its' reflexive form -
⮞ This situation - it's just a dream that came true!
המצב הזה - זה פשוט חלום שהתגשם! (audio #5)
⮞ Sometimes it's sad when a dream comes true - one doesn't know what to do afterwards.
לפעמים זה עצוב כשהחלום מתגשם - לא יודעים מה לעשות אחר כך. (audio #6)
⮞ Midnight - it's a magic time when all the wishes come true.
חצות - זה זמן קסום כשכל המשאלות מתגשמות (audio #7)