The Portuguese 21-year-old arrived in the UK on Thursday as a £6million deal was being formulated to capture him from Benfica.
Moyes said: "Manuel had the first part of his medical yesterday and that will be completed today. I would then expect him to become an Everton player within the next 24 hours."
The move will not been completed in time for him to acquire international clearance to be involved in Saturday's Premier League trip to Reading.
Everton have also had to make very sure their contract to acquire Fernandes has been cleared by the Premier League.
Fernandes is represented by the same companies that brought Carlos Tevez and Javier Mascherano to West Ham last summer, sparking the months of wrangling over the clauses of their third party ownership.
Everton, it is believed, are only buying 50% of the player from Benfica, with third party companies owning the rest.
The contract has been constructed in much the same way as the ones that allowed Liverpool and Manchester United to acquire Mascherano and Tevez, but clearly without the controlling clauses that have caused West Ham so much trouble.
Everton will have an option to buy out the rest of the player after a fixed time scale.
Moyes said: "Manuel was with us on loan last season, so he knows all about us and we hope he will be able to hit the ground running when he arrives.
"He knows about us and what we do, he will give us a different option. We are playing with Lee Carsley and Phil Neville just now in the centre of midfield and he will give us more competition there.
"But he is a different type of player, with a bit more craft. At 21 he was a big player in the European Under-21 championships for Portugal and we are delighted to have him."