Gary Cahill and John Terry, both of Chelsea, were selected at centre-back in the Premier League selection, but Martinez feels that Jagielka was cruelly overlooked.
The Spanish boss has suggested that the England international performs a very demanding role at Goodison Park and that he deserves more recognition for the consistent high-level performances that he puts in.
"When you are looking at the awards at the end of season I think people get affected by winning teams and teams that have caught you eye by the results more than anything," he said.
"Any football person that has gone into detail and seen what Phil Jagielka has done this season, undoubtedly he should have been in the PFA Team of the Year. He’s not just a defender defending; he’s a defender who has been a leader of men and been a captain through difficult periods.”
Everton's defensive record has not been particularly impressive this season, and that may be part of the reason why Jagielka missed out.
The Toffees have failed to shut out opposition teams successfully, but it is true that Jagielka has had a good season.
The experienced centre-back has helped to guide John Stones through matches and the pair now look to have formed a solid partnership at the heart of Everton's back four.
It is a foundation that Everton can build around next season, as Martinez looks to strengthen his squad by making some important additions over the coming months.