O menino coça-se quando tem comichão no braço.

Coça-se is from the verb coçar-se, which means to scratch oneself.

• coçar = to scratch
• coçar-se = to scratch oneself

So in this sentence, O menino coça-se means The boy scratches himself.

The se is a reflexive pronoun. It shows that the action comes back to the subject.

So:

• O menino coça o braço = The boy scratches the arm / his arm
• O menino coça-se = The boy scratches himself

In European Portuguese, reflexive pronouns are often attached to the verb with a hyphen in normal affirmative sentences, which is why you see coça-se.

In European Portuguese, this is the normal pattern in many affirmative main clauses: the object/reflexive pronoun comes after the verb and is joined with a hyphen.

So:

• coça-se
• lava-se
• chama-se

This is called enclisis.
A learner used to Spanish or Brazilian Portuguese may expect the pronoun before the verb more often, but in Portugal Portuguese, verb + hyphen + pronoun is very common.

Portuguese often expresses this idea as scratching oneself when there is an itch.

So the sentence is focusing on the reaction:

• O menino coça-se = The boy scratches himself

If you want to talk about the sensation itself, Portuguese can use other structures, such as:

• O braço tem comichão = The arm itches / the arm has an itch
• O menino tem comichão no braço = The boy has an itch in his arm / on his arm

So this sentence combines both ideas:

1. he scratches himself
2. when he has an itch on his arm

Ter comichão is a normal Portuguese way to express to feel itchy or to have an itch.

So:

• ter comichão = to have an itch / to feel itchy
• tem comichão = has an itch / feels itchy

This is one of those expressions that does not match English word-for-word. English often uses itch as a verb, but Portuguese commonly uses ter + comichão.

Comichão means itch, itchiness, or an itching sensation.

It is a very common word in European Portuguese.
A learner may also come across coceira, which is much more common in Brazilian Portuguese.

So for Portugal Portuguese:

• comichão = the usual word you should learn first

Because no is a contraction:

• em + o = no

So:

• no braço = in/on the arm

Portuguese very often contracts prepositions with articles:

• em + o = no
• em + a = na
• de + o = do
• a + o = ao

So comichão no braço is the natural form, not comichão em o braço.

Portuguese often does not use a possessive where English would.

So:

• tem comichão no braço naturally means has an itch on his arm
• it is understood that it is his arm because the subject is the boy

Adding a possessive is possible in some contexts, for example no seu braço, but it is often unnecessary and can sound less natural here.

In Portuguese, nouns are very often used with an article where English would not use one.

So:

• O menino = The boy

If you say just menino, that usually would not work as a complete subject in a normal sentence like this. Portuguese prefers the article here.

Quando means when.

It introduces the time clause:

• quando tem comichão no braço = when he has an itch on his arm

So the full structure is:

• O menino coça-se = main clause
• quando tem comichão no braço = time clause

Together: The boy scratches himself when he has an itch on his arm.

Portuguese often leaves out subject pronouns when the verb form already makes the subject clear.

Here:

• tem = he/she has

Because the subject is already understood from O menino, Portuguese does not need to repeat ele.

A fuller version would be possible in some contexts:

• O menino coça-se quando ele tem comichão no braço

But that is less natural unless you want extra emphasis or contrast.

Yes, but it is slightly different.

• O menino coça-se = The boy scratches himself
• O menino coça o braço = The boy scratches his arm / the arm

The version with coça-se focuses on the boy performing the action on himself.
The version with coça o braço names the body part directly.

Both can be correct depending on what you want to emphasize.

The ç is pronounced like s.

So:

• coça sounds roughly like KOH-sa
• coça-se sounds roughly like KOH-sa-suh in European Portuguese, though the final vowel is usually very reduced

A few useful pronunciation notes:

• ç = s sound
• o in unstressed position in European Portuguese is often reduced
• -se at the end is usually not pronounced like a full English say

Roughly, comichão sounds like koo-mee-SHAWN or koh-mee-SHAWN, depending on accent and reduction.

Important parts:

• ch in Portuguese usually sounds like sh
• ão is a nasal sound, common in Portuguese, and does not exist exactly in English

So the final syllable is not a plain own sound. It is nasal: -chão.

Yes, it is natural and grammatically correct in European Portuguese.

It uses several very typical features of Portugal Portuguese:

• the reflexive form coça-se
• enclisis with a hyphen
• ter comichão for to feel itchy
• omission of the possessive in no braço

So it sounds like a normal, idiomatic sentence.