I’m having some trouble memorizing which reading is on’yomi and which is kun’yomi. Do you guys have some pro tips to help with this? 
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Welcome to the site!
Firstly, I would recommend not worrying about it too much. There are some rules of thumb, but most people just get a feel for which is which over time.
Because of the origins of kunyomi and onyomi, with kunyomi originating from older forms of Japanese and onyomi coming from Chinese, certain readings never appear in one category or the other.
For instance, an onyomi will never be more than 2 mora long. So anything like こころ, ひるがえ, いしずえ, etc., has to be kunyomi because of that rule.
When お sounds are lengthened, typically they are spelled with an う if it’s onyomi, and an お if it’s kunyomi. So the しょう and こう readings you will see all the time are onyomi, and things like こおり and とお will be kunyomi readings.
Some things, like single mora readings, are basically impossible to know for sure without checking or learning the vocab. So things like し, か, etc., could be either one. You just have to check. By coincidence some kanji can share an identical on and kun reading. For instance, the character 架 has an onyomi of か and a kunyomi of か.
Just keep plugging along and you’ll get a feel for them.
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Thanks a lot for this, it will help for sure 
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That was hugely helpful for me as well.
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Great explanation.
As he also said, though, knowing which is which isn’t a big deal, specially for WK. The site will not punish you for writing out one when you should do the other. It’ll just warn you it wants the other reading instead.
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Also, if you know some vocabulary with the specific kanji in there, you can often extract the kun and on reading from there.
That is not entirely true. When you see the kanji on it’s own with a purple background the site expects you to put the kun’yomi and it will punish you(mark wrong answer) if you put the on’yomi instead.
For example when you see 水 with a pink background Wanikani wants the on’yomi (すい) and will warn you without ‘punishing’ you if you write みず, when however the background is purple you won’t get any warning if you write すい and it’ll be marked wrong instead.
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That is different, though. Purple background is not a kanji reading but a vocab WORD. It only has one answer and is not ambigous. It wouldn’t make sense to get a second chance on verbs either if you accidentally but the onyomi. The reason WK gives you a second chance in kanjis is because both readings are technically a correct answer, but WK sometimes uses one or the another.
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That’s not really about knowing on vs kun though. When it’s a purple background it wants you to enter the reading of the word. In most cases for single-kanji words this will be the kun’yomi, but just like learning the reading of any other word, it’s about knowing that the word for water is みず.
It marks you wrong (without any ‘warning’) because you don’t say the word 水 ‘すい’.
Although you will gradually get a feel for on’yomi vs kun’yomi naturally and it helps to infer how to read different words, it’s not worth worrying about specifically memorising on’yomi and kun’yomi for each kanji from the start. That’s the whole reason WK teaches extra readings via vocabulary; to help you avoid that headache.
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I know that, but that means you do need to know the difference and which is which. The word reading is the kun’yomi, and if you don’t know which the kun’yomi is you’ll get the answer marked wrong.
Yes, and WORDS are read with the kun’yomi reading. So if you can’t distinguish between the two you’ll get an error and no warning. I’m not saying that this behaviour is undesirable, but that also means that it is important to know which reading is which.
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Just to clarify, there are lots of vocab words that use the onyomi, and entering the kunyomi would be wrong (for the vocab being taught). For just a few, 点 (for “point”, てん is correct and つ is wrong), 本 (for “book,” ほん is right and もと is wrong), 用 (for “task,” よう is right and もち is wrong).
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I think we’re just arguing semantics.
I didn’t start out thinking “this is a single-kanji word, therefore it must be kun’yomi, therefore the answer is X”.
I just learnt the word. The important aspect for new users is to realise they don’t need to stress too much about these things to start with, as it will come naturally. That way you’re also less likely to get in tangles over exceptions when they crop up.
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I’m not saying one should stress about it, I’m just saying that one can’t assume that when the website asks for a reading one can just put a random one between kun and onyomi and expect to get a warning if the other one was required, as this only works for kanji’s, whereas with vocabulary only the correct reading is accepted. No reason to stress, but useful to know imho.
Likewise, memory only goes so far without some other aids and patters. Most vocabulary uses the kun’yomi, so if one knows the difference and can’t remember that specific word you can take an educated guess and be right most of the times (although as Leebo pointed out there are exceptions).
Romance languages have a lot of verb endings that follow some rules (regular conjugation), but there are a lot of exceptions too. Rather than memorising every single thing is much easier to memorise the general rules and remember the exceptions for what they are, I think the same applies to readings.
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This makes it so much easier to understand now. Thank you! So much knowledge in these forums!
As others have pointed out, Vocabulary is unambiguous, therefore, you don’t have options to choose from.
Many vocabulary words will actually sound nothing like both the kun or on yomi that you have learned before with the Kanji, as WK doesn’t teach you every single reading at once. That means that, for Vocabulary, you’ll always have to learn that particular reading on its own.
I think it comes with time, but if it helps, one of my native Japanese teachers back in high school straight up told me that the majority of Japanese people don’t know the difference between the two.
He said that most Japanese natives just memorize the reading for each word/verb and just have a gut feeling for the readings.
He could be wrong, but that would go along with what my university teachers have said as well.
Basically, I wouldn’t worry too much.
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The easiest way to learn which reading is on’yomi or kun’yomi (without any extra time or effort) is to install [Userscript] WaniKani Katakana Madness. All of the pink kanji reviews will display your reading answers in katakana for on’yomi. If you get far enough with WK, easily distinguishing between the two becomes second-nature 
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It’s funny… some of the vocab is starting to come together for me like that as well… I just seem to know when something doesn’t sound quite right or doesn’t have the right “flow”. It’s saved me on a few reviews actually.
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The problem I had with this script seemed that even with the kanji that used kunyomi in the kanji questions had katakana. I think.