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I searched for both they mean to wake up.

When do I need to use 目覚める and 起きる.

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Don't forget to add 起床 to your list. (meaning to get up and out of bed. – paullb Jul 31 '14 at 5:40
up vote 4 down vote accepted

起きる literally means "to get up", while 目覚める means "(your) eyes are opened". This can mean either literally (i.e., waking up from sleep) or metaphorically (come to one's senses, come to a realization).

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Though that doesn't mean Okiru cant or isn't used metaphorically. – user6915 Jul 29 '14 at 21:15

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