The 2012 All Australian ruckman had a wretched 2013 season, battling groin soreness throughout.
He started the previous pre-season late due to groin surgery in November last year and missed the first five rounds.
He played 11 matches before succumbing to soreness in round 18 and was rested for the remainder of the year.
Naitanui has trained hard on his own throughout September and October to ensure his body is right for the pre-season and Simpson believes he will be ready to go.
"He's definitely running now - I think he's pain-free," Simpson said.
"So, touch wood, he's right to go. We'll manage him as well. He's pretty keen to make a pretty good first impression, so we'll make sure we manage his loads, but at the moment he looks OK."
The unknown for the Eagles is Beau Waters. The vice-captain managed just seven matches last season as he battled various injuries. He missed a month early in the year due to a quad strain. He then required a knee arthroscopy before his season was ended by shoulder surgery.
There have been reports that complications following that surgery could delay Waters' start to pre-season and Simpson was unsure of his start date.
"I haven't spoken too heavily with the fitness department on who we have to manage," Simpson said.
"There are definitely players there who are quite vulnerable to injury so we will keep an eye on that."
Pre-season began for the first to fourth-year players on Wednesday with skills and fitness testing.
Young key-position prospect Jeremy McGovern tested below some of the minimum requirements and will be required to do a tailored training program to get up to speed before the full squad begins on November.
The 21-year-old was upgraded from the rookie list recently but is yet to play a senior game. He played a key role in Claremont's 2012 WAFL premiership but had his 2013 campaign derailed by an early season ankle injury before he required season-ending hip surgery in July.
