On 23 April 2017, he secured 20.0% of the votes at the first round of the French presidential election, arriving third, and failing to enter the runoff.
François Fillon has spoken at a wide variety of universities in Britain, notably King's College London and the London School of Economics. On 1 September 2017, Fillon became a partner at asset manager Tikehau Capital.
In January 2017, Le Canard enchaîné published an article in which Penelope Fillon was accused of alleged fictitious employment, as her husband's "assistante parlementaire" for a total salary of €500,000 over eight years on the one hand, and as a "literary adviser" of Revue des deux Mondes on the other, with a monthly salary of €5,000, amounting to a total of another €100,000. A preliminary hearing immediately opened. The public outcry around this so-called "Penelopegate" was such that doubts were voiced about François Fillon himself, who was the frontrunner for the 2017 presidential election, with an immediate sharp decline in the opinion polls.
On 31 January, new reporting by Le Canard enchaîné found that Penelope Fillon was actually paid €300,000 more than previously reported, for a total sum of €831,440 for 15 years of her parliamentary assistant work. It also reported that Fillon had paid two of his children €84,000 for little apparent actual work. On 6 February 2017 Fillon held a press conference. He said "It was a mistake and I apologize to the French [people]" but also said that the salary of his wife was "perfectly justified".
On 3 March 2017, the OCLCIFF (Central office for the fight against corruption and financial and fiscal crime) executed a search at the Manoir de Beaucé where François and Penelope Fillon reside in the Sarthe department. This followed a search by the same agency on 2 March 2017 at the Fillons' Paris residence in the 7th arrondissement. On 6 March 2017, the inner circle of Fillon's party had a crisis meeting. Beforehand, Alain Juppé had definitively excluded becoming a replacement candidate. Fillon continues his candidacy, despite his promise (given on 26 January on TV) to withdraw from the race if subjected to criminal prosecution. On 23 March, Fillon said on national television that Bienvenue Place Beauvau, a book co-authored by Didier Hassoux of Le Canard enchaîné, suggested President François Hollande ran a shadow cabinet to spread rumours about his opponents. Hassoux denied this was the case.