It was his first chance of cutting and changing the squad to his liking after coming in to replace Kit Symons at the end of December and making sure the side remained in the Championship.
It was a big summer and one that many saw as weakening the team, rather than improving it with the departures of both Ross McCormack and Moussa Dembele.
As it turned out, that wasn't the case and Fulham finished in a very respectable 6th place, losing out on contesting the final at Wembley courtesy of a 2-1 aggregate defeat to Reading.
There's the possibility that the bigger clubs will come looking for Fulham's best talent again this summer, with Newcastle hovering about Tom Cairney while Tottenham are looking to turn Ryan Sessegnon into the next Gareth Bale.
If the worst does come to pass, Fulham fans can take hope that despite losing a lot of talent last summer, the squad did a lot better than most of those that left.
Except that invincible, of course.
Here's how they all got on away from Craven Cottage this season.
Ross McCormack (Aston Villa, £12million)
What happened? Fulham parted ways with their top scorer for a hefty fee, with McCormack wanting to play in the Premier League - Villa was his way to do so.
Did it work out for Fulham? They received a decent fee for their top scorer and after the season McCormack has had, it has probably worked out well for the Cottagers. Despite losing him they were the joint top scorers in the division, so it has to be said the effects of losing McCormack weren't nearly as bad as first feared.
Did it work out for McCormack? In a word, no. He was dropped by Steve Bruce for not being fit enough to play for Villa and was then shipped out to Nottingham Forest in February until the end of the season.
Konstantinos Mitroglou (Benfica, £6million)
What happened? Fulham signed Mitroglou in January 2014 for £12million, but never played under Felix Magath before being loaned to Olympiacos. He was then loaned to Benfica, where he scored 34 goals in 2014/15 which moved the Lisbon club to sign him permanently.
Did it work out for Fulham? Well, after a horrendous time at Craven Cottage he was never really happy at the Cottage, and despite signing him for a hefty fee it was a case of cutting their losses with Mitroglou and getting him off the wage bill.
Did it work out for Mitroglou? Big time - the Greek was in the form of his life this season and banged in 16 goals for Benfica as they won the Portuguese first division by six points. He's even been linked to a big money move to China.
Maarten Stekelenburg (Everton, Undisclosed fee)
What happened? The Dutchman signed for Everton having spent two seasons away on loan, firstly at Monaco and then at Southampton. Everton came in for him and on July 1 he signed for them on a three-year deal.
Did it work out for Fulham? Stekelenburg hadn't played for the Cottagers since losing his place in the side under Magath, who favoured Marcus Bettinelli and Jesse Joronen over the Dutch international. Having not played for the side for so long, it made sense that Fulham moved him on, with David Button arriving from Brentford.
Did it work out for Stekelenburg? He had a decent season but a mixed one at that and could only be their second choice next season. He produced a heroic display at the Etihad where he saved penalties from both Sergio Aguero and Kevin De Bruyne.
Matt Smith (QPR, £500k plus incentives)
What happened? Smith was sold to QPR in January on the final day of the transfer window, having only scored twice for Jokanovic's side. He wasn't the type of player the Serbian liked and it caused a bit of uproar around the Cottage when it was announced.
Did it work out for Fulham? Smith wasn't getting games, and despite the need for a striker he wasn't going to get games in the side - especially with Fulham scoring as many goals as they did. All in all, I think it probably did work out for Fulham.
Did it work out for Smith? He's found a new lease of life at QPR, where he is starting regularly and managed to get himself four goals since signing, so it's worked out well for him.
Ben Pringle (Preston, Undisclosed fee)
What happened? Pringle signed for Fulham from Rotherham in 2015 after a very good season for Rotherham, but he didn't suit the style of play Jokanovic wanted the side to play and he was eventually shipped off, first to Ipswich on loan and then to Preston permanently.
Did it work out for Fulham? Pringle wasn't really good enough for Fulham, so selling him to Preston was the best move for the club. They didn't miss him either and he was never going to get into the side this season.
Did it work out for Pringle? Not particularly - he was a bit part player in the Preston side and only played 14 games this season, without scoring a single goal for the club. He's been linked with a move back to Rotherham this summer.
Fernando Amorebieta (Sporting Gijon, 300k Euros)
What happened? Having failed to lock down a regular starting place, Amorebieta found himself shipped out on loan to Middlesbrough twice before being sold to Sporting Gijon.
Did it work out for Fulham? Although he played in the Premier League with the club and nearly got promoted with Middlesbrough, he wasn't favoured by the management and with Tim Ream and Tomas Kalas in front of him, as well as the arrival of Ragnar Sigurdsson, he was never going to get a game.
Did it work out for Amorebieta? He had a decent season personally in Spain where he played 27 times as Gijon finished 18th in La Liga, but he couldn't help them avoid the drop.
Jazz Richards (Cardiff, swap deal for Scott Malone)
What happened? Fulham swapped Richards to Cardiff for Scott Malone, with Jokanovic preferring Ryan Fredericks at right back instead of the Welshman.
Did it work out for Fulham? It sure did - Fulham got a great deal and Malone proved to be one of their best signings, going on the make it into the team of the season.
Did it work out for Richards? He got injured in September for three months but returned in January, but made 29 appearances in all for the Welsh side. There are still arguments as to why got the better deal between Cardiff and Fulham in this deal.
Dan Burn (Wigan, free transfer)
What happened? Burn was released at the end of his contract despite becoming a first team regular under Jokanovic, making 35 appearances before going to join Wigan.
Did it work out for Fulham? Another one who probably wasn't good enough to hold a regular starting spot in Fulham's XI this season - the side never missed him so it worked out well for Fulham.
Did it work out for Burn? He won the club's Player of the Year award, but despite that couldn't help Wigan as they were relegated back to League One.
Moussa Dembele (Celtic, £500k)
What happened? Fulham's sought after teenager signed for Celtic when his contract expired having scored 17 goals in all appearances for the club.
Did it work out for Fulham? Not really - he was going to leave but Fulham missed out on a huge transfer fee for the youngster and Dembele is now being tipped to leave the club for fees of 30m.
Did it work out for Dembele? It did - he went on to make history as he became an invincible with Celtic, winning the treble without losing a single game all season. He's now being linked with Europe's best clubs as he looks to go on and make a real name for himself.
Others who departed: Andy Lonergan, Emerson Hyndman, Jamie O'Hara, Alexander Kacaniklic, Sakari Mattila, Shaun Hutchinson, Ange-Freddy Plumain and Adam Taggart.