Ako bude prekasno za vlak, prenoćit ćemo u Rijeci.

After conjunctions like ako (if), Croatian normally does not use će + infinitive in the subordinate clause. Instead, it uses the budem form of biti for future reference.

So:

• ako bude prekasno = if it is / if it turns out to be too late
• not normally ako će biti prekasno

This is a very common pattern in Croatian:

• Ako bude vremena, doći ćemo. = If there is time, we’ll come.
• Ako bude kiše, ostat ćemo doma. = If it rains / if there is rain, we’ll stay home.

So in your sentence, bude points to a possible future situation.

Bude is the 3rd person singular form from the budem set of forms of biti. These forms are often used in clauses that refer to the future, especially after words like ako, kad, čim, and similar conjunctions.

Here the subject is impersonal, like English it in if it’s too late, so Croatian uses singular bude:

• ako bude prekasno = if it is too late

There is no visible subject word, but the idea is still it in the general sense.

Because this is an impersonal expression: it is too late.

In Croatian, when no specific noun is being described, the neuter singular form is often used:

• kasno je = it is late
• prekasno je = it is too late
• hladno je = it is cold
• jasno je = it is clear

So prekasno is the natural form here. It is not agreeing with vlak. It belongs to the whole idea it is too late.

After za in this meaning, Croatian uses the accusative case.

So:

• za vlak = for the train

The noun vlak is masculine inanimate, and in the singular its accusative form is the same as its nominative form:

• nominative: vlak
• accusative: vlak

So the case does change grammatically, but the form happens to stay the same.

Here za vlak means for the train, in the sense of too late for the train or too late to catch the train.

So the phrase:

• prekasno za vlak

means:

• too late for the train
• idiomatically, too late to catch the train

It does not mean movement toward the train. It is about whether the train can still be caught.

It is the future I form of prenoćiti (to spend the night / stay overnight).

Croatian forms future I with the infinitive plus the clitic forms of htjeti:

• ću, ćeš, će, ćemo, ćete, će

With many infinitives ending in -ti, standard spelling drops the final -i before these clitics:

• prenoćiti + ćemo → prenoćit ćemo
• raditi + ću → radit ću
• vidjeti + ćemo → vidjet ćemo

So prenoćit ćemo is the standard written form.

Because Croatian often leaves subject pronouns out when they are not needed. The verb ending already shows the person and number.

In prenoćit ćemo, ćemo tells you that the subject is we.

So:

• prenoćit ćemo = we will spend the night / stay overnight

You could add mi for emphasis:

• Mi ćemo prenoćiti u Rijeci.

But in a neutral sentence, Croatian usually omits it.

Because u meaning in a place takes the locative case when it shows location.

So:

• Rijeka = nominative
• u Rijeci = in Rijeka

Compare:

• u Rijeci = in Rijeka, located there
• u Rijeku = to Rijeka, motion toward it

In your sentence, the meaning is location, so u Rijeci is correct.

Yes, aspect is important.

Prenoćiti is a perfective verb, and it means to spend the night once, as a complete event. That fits this sentence well, because it refers to one future overnight stay.

So:

• prenoćiti = to stay overnight, once / as a completed event

If you wanted a habitual or repeated meaning, Croatian would normally use an imperfective verb instead.

In this sentence, the idea is a single result of the condition:

• If it’s too late for the train, we’ll stay overnight in Rijeka.

That is why the perfective verb works naturally.

Yes. Croatian word order is fairly flexible.

The sentence you have is very natural and neutral:

• Ako bude prekasno za vlak, prenoćit ćemo u Rijeci.

But other orders are possible, for example:

• Prenoćit ćemo u Rijeci ako bude prekasno za vlak.
• Ako bude prekasno za vlak, u Rijeci ćemo prenoćiti.

The meaning stays basically the same, but the focus can shift slightly. The version with the ako clause first is a very normal way to present the condition before the result.

Because the sentence begins with a subordinate ako clause:

• Ako bude prekasno za vlak = the condition
• prenoćit ćemo u Rijeci = the main clause

In Croatian, when a subordinate clause comes before the main clause, it is separated by a comma. So the comma here is standard punctuation.

Yes, but the meaning shifts slightly.

• Ako bude prekasno za vlak looks forward to a future situation: we do not yet know whether it will be too late.
• Ako je prekasno za vlak sounds more like a present or already-assessed situation: if it is too late for the train.

So in a plan about a future possibility, ako bude prekasno is the more natural choice.