The illegal assembly charge relates to a banned anti-government march on 31 August, which Mr Lai is accused of attending.
The intimidation charge relates to a clash with a journalist in 2017.
The newspaper Mr Lai founded, Apple Daily, is frequently critical of Hong Kong and Chinese leadership.
Two other pro-democracy figures, politicians Lee Cheuk-yan and Yeung Sum, were also arrested on Friday.
They have also been charged with one count of illegal assembly in relation to the same protest.
Senior Superintendent Wong Tung-kwong said all three men would be called to the Eastern Magistrate Court on 5 May.
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