理由 and 原因: reasons for choices and causes of events
Distinguish reasons explaining actions from causes producing events, including contexts where they overlap.
Reasons explaining an action
理由 is read りゆう and gives grounds explaining a choice or judgment. 「この仕事を選んだ理由を教えてください」 asks why the person chose this job.
「理由があって断りました」 says that the speaker refused for a reason. The sentence alone does not reveal the specific reason or whether it was justified.
Causes producing an event
原因 is read げんいん and refers to a factor that produced an event or condition. 「故障の原因を調べています」 describes an ongoing investigation into the cause of a malfunction.
「原因はまだ分かりません」 says that the cause is not yet known. It neither denies that a problem exists nor identifies a particular person as the cause.
Different focuses behind similar translations
「遅れた理由」 can focus on explaining why someone was late, while 「遅れの原因」 can focus on analyzing what caused a delay. Both might refer to the same traffic jam, so the distinction is not absolute.
原因 often occurs with negative situations such as malfunctions or accidents, but it is not exclusively for bad events. First ask whether the focus is a motive for choosing or a factor causing something.
Which word naturally fills 「応募した（ ）を教えてください」 when asking about an applicant's motivation?
Show the answer and why
理由 is natural. The question asks about the motivation behind applying, rather than analyzing a causal factor as 原因 would emphasize.