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I wanted to say: there is a pen. Hence, I said ペンはある。But my girlfriend said to me that one has to say: ペンがある。But she can't explain to me why, and I don't understand.

Do you have an explanation?
Thanks in advance!

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    We usually say 「XXある(よ)」(は=topic particle) etc when replying to 「XXはある?」"Is there XX?", and 「XXある(よ)」(が=subject particle) when replying to 「何がある(の)?」"What's there?" – Chocolate May 22 '16 at 3:50
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I feel that the distinctions between は and が are one of the hardest parts to learn about the Japanese language, so I'll try to keep things mostly focused on this example.

ペンはある

Here "は” marks ”ペン" as a "topic", rather a "subject", but what that really translates into is a feeling of:

There is a pen (but there isn't a ....)

This is because that "は" also is commonly used to indicate that what follows it applies to the thing before the は, but not to something else which may or may not be directly stated.

Here is an example where the thing that doesn't apply is directly stated:

ペンはあるけど、鉛筆はない

In fact は tends to be used more frequently with negative verbs (hence the は part of ではない). So if you are saying "the pen isn't there", this would be completely natural:

ペンはない

However, if there was a situation where someone was panicking and somebody asked them "What is wrong?" (どうしたの?), they could very well reply using が instead:

ペンがないよ!

This is because が strongly emphasizes the subject, and is generally used when there was some uncertainty about a subject which is being clarified.

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    The reason why you use が (or save topicalization) in the last example is because it's a sentence of neutral description rather than emphasis by a sentence of exclusion. In short, you can't rephrase it as ないのはペンだよ. – user4092 May 22 '16 at 7:24
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That would be 「ペンある。」 100% of the time.

「ペンある。」 (= "There is a pen.") is a statement about 'what is there' or 'what the speaker has just found at a particular location". It is not a statement that gives some kind of description about either pens in general or a particular pen.

If you desire to make a further statement about the pen after you have found it and said 「ペンある。」, you can use 「」 as in 「そのペンとても[長]{なが}い。」= "The pen is very long." and such .

「ペンある。」, as a stand-alone statement, sounds far more weird to us Japanese-speakers than you could probably imagine at this stage. You could look like you were trying a make a profound philosophical statement about pens in general. I call that the power of particles - "POP" for short. Learning Japanese means learning POP.

If you go outside of your house and find a dog right in front of you, you will say 「イヌいる。」. If you said 「イヌいる。」 instead, people would wonder if you were OK because you would look as if you were making a metaphysical statement about dogs and the universe outside of your front door on your way to Burger King.

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