Can this query be optimised with indexes, or should I change my schema?
I think this request is fully optimized on a SQL point of view. Meanwhile, you may can increase performance by choosing a particular type of index depending on your data (for example BINARY for IDs), check this documentation for more details.

Moreover you have to keep in mind that the innoDB engine in MySQL (if you're using it) may be slow on a big amout of data.