The head civil servant is the Secretary of the Cabinet (Sir Gus O'Donnell) with the next grade being Permanent Secretary, or officially Permanent Under-Secretary of State, and these posts exist in each government department.
There is an argument that says that technically the Comptroller & Auditor General (Sir John Bourn) is the most senior because he reports to Parliament via the Public Accounts Committee and not to a Minister or to any other civil servant. However, as said by others, the Cabinet Secretary is the head of the paid civil service.