Most of the major sites in Athens fall within a single square-mile block centered on the Acropolis. The National Archaeological Museum is the exception that proves the rule.
It is located about a mile and a half due north of the Acropolis. Hop the Metro (Lines 1 or 2) to Omonia Square. A block east of the Square is 28 Octovriou Street. Follow this north for 8-10 blocks and you’ll see the Museum looming up on your right. Alternatively, take the Metro (Line 1) to Victoria Station. Walk east on Heiden Street and turn right on 28 Octovriou. Go 5 or 6 blocks. The museum will be on your left.