Fabregas began with a bang last term after returning to his boyhood club but his form tailed off and Vilanova's predecessor Pep Guardiola overlooked him for some key matches in the Champions League and La Liga.
The 25-year-old performed well for Spain at Euro 2012 playing in a roving forward role but has yet to make much of an impression for Barca this season and watched Wednesday's Spanish Super Cup defeat to arch rivals Real Madrid from the bench.
"The second year is always better," Vilanova told a news conference previewing Sunday's La Liga match at home to Valencia when asked about Fabregas's form.
"I am convinced he will have a great season," added the 43-year-old, who was promoted from assistant coach when Guardiola announced he was leaving the club at the end of April.
Barca's Brazilian full-back Dani Alves trained normally on Saturday and may be available for the Valencia game after pulling out of Wednesday's Super Cup return leg at the last minute due to a leg injury.
Vilanova said a decision would be taken on Sunday as to his fitness and he would also consult club doctors on whether to risk captain Carles Puyol, who fractured a cheekbone in last weekend's 2-1 La Liga win at Osasuna.
The Spain centre-back will have to wear a face mask if he features at the Nou Camp as the early leaders look to maintain their 100 percent start to the season.
