The SQLite CLI shell provides no way to clear the history. It keeps the history internally (in process memory), so nothing you do to its persistent form will affect that for the readline library written as it is today. You may want to consider using one of the many excellent GUI tools for manipulating and querying SQLite databases. Maintaining a set of save queries is an extremely common feature in such tools. The CLI shell is not really meant to be a deluxe tool. It is more of a bare-metal interface to the SQLite library, (although less so than in years past.)