Learn Hardcore Japanese: apuri de ryoukin o keisanshimasu.

It marks the means or place of the action. Here it means “by means of/using,” so アプリで = “using the app.” You could make the “using” idea explicit with アプリを使って料金を計算します. If you want to highlight “inside the app,” say アプリ内で.

Why is を used with 料金?

Because 計算する is a transitive verb and takes a direct object marked by を. So 料金を計算します = “(I) calculate the fee.” In passive voice the fee becomes the subject: 料金が計算されます. You can also topicalize: 料金は（アプリで）計算します where は replaces を to mark the topic.

Can I change the word order?

Yes. Both are natural:

アプリで料金を計算します。
料金をアプリで計算します。 Japanese relies on particles, not fixed order. The second puts a bit more focus on 料金 by mentioning it earlier, but both are common.

Who is doing the calculating? There’s no subject.

Japanese often omits subjects when obvious from context. 計算します could mean “I/we/you/they will calculate,” depending on the situation. If you need to specify:

“I”: 私はアプリで料金を計算します。
“This app”: このアプリは料金を計算します。 (or with が: このアプリが…)

Is this present or future?

The non-past 〜します covers both habitual and future.

Habit: いつもアプリで料金を計算します。
Near future / decision: 今からアプリで料金を計算します。 For an ongoing action right now, use 〜ています: 今、アプリで料金を計算しています。

Should it be アプリで or アプリに if I mean “on the app”?

Use アプリで for “on/with (the app)” as the tool or place of the action. アプリに doesn’t work for “using an app.” If you want to emphasize “within the app interface,” say アプリ内で. To say “using,” アプリを使って is also common.

Is 計算する a noun + する verb?

Yes. 計算 (calculation) + する (do) forms the verb “to calculate.” Dictionary form: 計算する. Polite: 計算します. You may also see 計算をする; adding を is a bit more formal/explicit but the meaning is the same.

Is 計算する the best verb here? What about 見積もる or 算出する?

計算する: general “to calculate/compute” numbers or amounts; perfectly fine with fees.
見積もる: “to estimate/quote,” often when the amount isn’t exact yet (e.g., project quote).
算出する: “to compute/derive,” more technical/formal.
割り出す: “to work out/figure out,” slightly colloquial. Choose based on nuance and formality.

What’s the difference among 料金, 値段, 金額, 費用, 代金, and 料?

料金: fee/charge for a service (train fare, admission, shipping).
値段: price of a product (price tag).
金額: monetary amount (the sum itself).
費用: cost/expense (often total costs).
代金: payment/price to be paid/charged (what you pay).
〜料: suffix “fee” (e.g., 入場料, 手数料). In this sentence, 料金 is natural.

If I want to say “The app calculates the fee,” is アプリで correct?

Make the app the subject with が: アプリが料金を計算します。 If it’s automatic, you can also say 料金が自動で（自動的に）計算されます。 アプリで focuses on using the app as a tool (someone uses it).

Can I drop を and say 料金計算します?

In casual speech or headlines/ads, dropping particles is common: 料金計算します is understandable. In normal writing or careful speech, keep を: 料金を計算します.

Why are there spaces? Are they normal in Japanese?

Standard Japanese doesn’t use spaces between words. The natural orthography is アプリで料金を計算します。 Spaces are sometimes added in teaching materials to help learners parse the sentence.

How do I adjust the politeness?

Plain: 計算する.
Polite: 計算します.
More formal/humble (to a customer): 計算いたします.
Friendly softening: 計算しますね。
Suggestion: 計算しましょう。 Choose based on who you’re talking to.

How do I say “can calculate” or make a request?

Ability: アプリで料金を計算できます。
Please calculate (polite request): アプリで料金を計算してください。
Even more polite: アプリで料金を計算していただけますか。／お願いいたします。

What’s the reading/pronunciation?

Romaji: Apuri de ryoukin o keisan shimasu. Kana/Kanji: アプリで料金を計算します。 Main words: アプリ (apuri), 料金 (りょうきん/ryoukin), 計算 (けいさん/keisan), します (shimasu).