It's a more formal way of saying "I didn't realise..." When I hear someone say, "Little did...," it's usually in the context of formal writing or speeches. E.g. novels, narrations on TV shows/films, etc. Another example is, "Little did I know..." This also just means, "I did not know..." I think the expression refers to you having little knowledge, or a small amount of knowledge, about something; so small that it is almost zero. I don't think you would hear that expression in a colloquial/informal conversation in English.