Anelka, 31, received the suspension after being sent home from the World Cup following a reported bust-up with the then-France coach Raymond Domenech.
The Chelsea striker blasted the FFF as "clowns" and laughed off the ban, insisting he had already retired from international football.
Ancelotti insisted Anelka did not deserve such a punishment and he said: "I think it was unfair for him - 18 games is too much.
"I don't know what happened there but Anelka is an honest man and he didn't deserve the decision.
"It is good news for myself because he can stay here to train during the international break, he can maintain a good condition.
"But for him it is not good news because every player wants to play in the national team.
"But Anelka has reacted very well. He has taken it with good spirit."
Anelka built up a reputation earlier in his career as a player who could be difficult to handle.
But asked whether Anelka has ever caused him any trouble at Chelsea, Ancelotti said: "No, never."
Anelka was not the only Chelsea star to endure a difficult summer - but there has been no World Cup hangover at Stamford Bridge.
Chelsea picked up from where they left off last season as Didier Drogba's hat-trick propelled them to a thumping 6-0 victory over West Brom on the opening day of the new Premier League campaign.
Roman Abramovich wants entertaining football and Ancelotti has delivered, with Chelsea scoring a record-breaking 103 goals last season. They banged in seven on three occasions before rounding off the campaign with an 8-0 thrashing of Wigan.
The two sides meet again at the DW Stadium on Saturday and the omens do not look promising for Wigan, who opened their season with a 4-0 defeat to newly-promoted Blackpool.
Ancelotti is anxious for Chelsea to set the Premier League pace from the outset - but he has also tried to temper expectations that tomorrow's trip to Wigan will be a walkover.
The Italian reminded Chelsea their first defeat of last season was at the DW Stadium.
Ancelotti said: "It is very important we make a good start, not just one game. Last year we won the first six games in the league and we want to do the same.
"I will be happy if we win 1-0. It is important to keep a clean sheet. Winning 6-0 or 7-0 every week is not football.
"It is important to win and to play well. We have to pay attention. The last game at Wigan we lost 3-1.
"We have to prepare well for this game and be right mentally. They caused us a lot of problems there last season, it was our first defeat, and we want to continue our good start to the season.
"They started the season badly and lost at home against Blackpool. They will want to be strong and have power tomorrow to produce a different game."
Ancelotti accepted the Brazilian striker Neymar will not be a Chelsea player after the in-demand 18-year-old decided to remain at Santos.
"I knew this. He was a Santos player, he is a Santos player. He is a young player and everyone looks at him but this doesn't mean he will be a Chelsea player," said Ancelotti.
Chelsea are looking to send Nemanja Matic and Slobodan Rajkovic out on loan before the transfer window closes.
Meanwhile, defender Sam Hutchinson, who made his first-team debut in 2007 but has been troubled by knee injury problems since, has announced his retirement.
Chelsea said the 21-year-old former England Under-19 international had suffered a recurrence of the knee injury and would work at the club's academy while taking a sports science course at university, before pursuing coaching qualifications.
Hutchinson made two Premier League appearances as substitute last season, and started in the Carling Cup match against QPR.