Remove all values duplicates from list
Iterating backwards was smart, but, yes, there is a much simpler way to do this using a list comprehension – this is how one typically filters a list in Python. 

filtered_words = [word for word in word_list if word != user_input]


Note that this creates a new list object rather than altering the original word list in place.

Your current code isn't terribly inefficient – it iterates over the list twice rather than once, but both are asymptotically linear. 

If you were to keep that structure, there are a number of small things that could be done to make the code more Pythonic. Compare the following loops to your own code:

for i, word in enumerate(word_list):
    if word == user_input:
        remove_queue.append(i)

for i in remove_queue[::-1]:
    del word_list[i]


These do the same thing, but are much more readable once one knows that enumerate can be used to iterate over both the index and element at once and that list[::-1] is a common method to iterate over a list backwards (albeit, slightly inefficient).

A final note is that I have updated all two-word names to use snake-case.