The metro also landed in the top spot in the nation for its expected growth rate in economic output this year.
Naples-Marco Island did well too, placing 11th for its anticipated job growth and sixth for its projected increase in economic output, or gross metropolitan product, in 2016.
Gross metropolitan product is the value of all finished goods and services produced. That can include anything from real estate commissions to restaurant sales.
"A lot of the growth we are seeing now is predicated on the post recession bounce back, which is still going strong," said Karl Kuykendall, a regional economist with IHS.
The new report was prepared for the U.S. Conference of Mayors. The annual rankings are based on year-over-year percentage increases.
A year ago, IHS ranked Naples-Marco Island first in the nation for its projected job gains in 2015, but the area's fall out of the top 10 metros this year shouldn't set off any alarms, Kuykendall said.
"Put simply the Naples economy has been coming back in recent years," he said. "Population has come back very strong, housing starts and construction have taken off and people are flocking to the metro area."
In 2015, Naples-Marco Island saw a job growth rate of 3.9 percent and it's expected to see another 3 percent increase this year. In 2015, the metro added 5,100 jobs and IHS predicts it will create another 4,100 this year.
Cape Coral-Fort Myers, a much larger metro area, added 8,600 jobs last year and it's expected to gain about 9,000 this year. It saw a growth rate of 3.7 percent last year and it's expected to see another 3.6 percent increase in jobs this year.
"There is one thing you've got to consider, the smaller the metro is, the easier it is to move the needle," Kuykendall said.
Naples-Marco Island and Cape Coral-Fort Myers have both come a long way since the Great Recession. Their job numbers didn't get back to where they were before the recession until the last quarter of 2014, Kuykendall said.
"They both recovered before Florida did overall, but the U.S. recovered faster, in the second quarter of 2014. It was close though. That's still impressive for Naples and Cape Coral, in the sense that their recessions were so much worse than they were for a lot of metros in the U.S. and they had a lot more area to recover."
Both metros saw job losses in the double-digits during the recession. "Cape Coral-Fort Myers and Naples-Marco Island were among the worst," Kuykendall said.
This year, IHS predicts the Cape Coral metro will see a 4.6 percent increase in its economic output to $26.2 billion, including adjustments for price changes. Naples-Marco Island is expected to see a 4.2 percent gain to $18.1 billion.
Both metros are benefiting from population growth, including retirees making their way to Florida.
In the Naples area, 28 percent of the population is 65 or older. In the Cape Coral area, the older demographic makes up 25 percent of the overall population.
IHS expects Naples-Marco Island to add 10,400 residents this year, bringing its total population to about 371,000. Meanwhile, Cape Coral-Fort Myers is projected to gain another 21,900 residents, for a total of about 727,000.
The tourism and construction industries continue to fuel growth in both counties too.
"One of the differences is that Naples tends to have higher incomes," Kuykendall said. "Maybe that's because they attract wealthier retirees. That's one of the key differences."