On 3 June, Brazilian Neymar was officially presented as a Barcelona player to more than 50,000 fans at Camp Nou. He joined the squad after the 2013 FIFA Confederations Cup in Brazil. On 20 June, after spending the previous season on loan to Mallorca, it was officially announced that Andreu Fontàs will be joining Celta de Vigo for a sum of €1 million. Barça will retain a buy-back clause in addition to the player's rights in any future transfer. While at Celta, Fontàs will be reunited with former Barcelona B coach Luis Enrique, whom he managed between 2008 and 2010. On 28 June, it was announced that Santos will participate in the 2013 edition of the Joan Gamper Trophy on 2 August at the Camp Nou. Santos' participation was agreed upon Barça signing Neymar.
On 6 July, Bojan was officially loaned to Ajax with an option for a second year loan spell. Bojan explained that conversations with Johan Cruyff had influenced his decision to move to Ajax, as well as the opportunity to play in the UEFA Champions League. On 8 July, Barcelona announced the transfer of Spanish international forward David Villa to Atlético Madrid for a reported fee of €5.1 million and reserve the right to 50% of any future sale of the player. Villa, who joined Barça in the summer of 2010, played 119 times and scored 48 goals and leaves the club after three seasons and eight trophies won. On 15 July, Barcelona announced that midfielder Thiago will be joining German champions Bayern Munich, where he joins his former Barcelona coach Pep Guardiola, for €25 million. The transfer also stipulates that the two clubs will play a friendly sometime within the next four seasons. The 22-year-old leaves after two season with the first team. On 16 July, it was announced that midfielder Sergio Busquets agreed to a contract extension with the club for a further five years until 2018, with an option of an additional year. Busquets' buyout clause remains set at €150 million. On 19 July, Barcelona President Sandro Rosell officially announced the resignation of current manager Tito Vilanova. Vilanova will not be able to perform his managerial duties as he undergoes further treatment for his illness. During the press conference, Rosell announced, "After evaluating the results from the routine check-ups, which Tito Vilanova underwent this week, he was presented with the option to continue treatment to control his illness which will make it impossible to continue his responsibilities as the first team manager of the senior side." As a result, Barça rescheduled their pre-season match against Lechia Gdańsk in Poland to 30 July. On 23 July, former Newell's Old Boys manager Gerardo Martino was officially announced as the new coach of Barcelona and is subsequently signed a two-year contract with the club. The appointment makes Martino, nicknamed "Tata", the fourth Argentine to coach Barça after Helenio Herrera, Roque Olsen and César Luis Menotti.
On 1 August, Cristian Tello extended his contract with Barcelona until 30 June 2018, with a set buyout clause of €25 million. On 18 August, Barcelona won their first match of the La Liga season thrashing Levante 7–0, with goals coming from Alexis Sánchez, Dani Alves and Xavi and braces by Lionel Messi and Pedro. On 25 August, Barça defeated Málaga with a single goal from Adriano before the half-time break. On 28 August, Barça won the 2013 Supercopa de España at the Camp Nou. The 0–0 scoreline at Camp Nou, meant that the 1–1 draw from the first leg at the Vicente Calderón was enough to win the trophy on the away goals rule, with the winning goal coming from Neymar's 66th-minute header.
On 1 September, Barcelona made it three wins in a row to ensure top spot on the league table, after a hard fought victory against Valencia. Messi's first half hat-trick, together with a match saving performance by Víctor Valdés, was enough to see Barça win at the Mestalla for the first time since 2011. On 14 September, Barcelona defeated Sevilla 3–2 at Camp Nou with a 94th-minute winner from Alexis Sánchez. On 18 September, Barcelona defeated Ajax 4–0 at home in their first group match of the 2013–14 UEFA Champions League with a hat-rick from Messi and one goal from Gerard Piqué. With the three goals, Messi took his career tally to 62 goals in the Champions League leaving him nine goals short of former Real Madrid forward and record marksman Raúl. He also became the first player to score four hat-tricks in the Champions League, whilst also netting his 24th such treble for Barça. On 21 September, Barcelona defeated Rayo Vallecano 0–4 at Campo de Vallecas. A hat-trick from Pedro, one from Cesc Fàbregas and another great performance from Valdés, who saved his second penalty in two consecutive matches, gave Barça the three points. This match also marked the first time since 7 May 2008 against Real Madrid where Barcelona did not finish the match with a higher percentage of possession than the opponent. Breaking a streak of 315 matches in a row. On 24 September, Barcelona continued its hot start to the league campaign with a 4–1 victory over Real Sociedad at home. On September 28, Barcelona defeated newly promoted side Almería on the road with a 0–2 scoreline. With the victory, Barça set a team record with seven wins from the first seven matches in the league. Messi scored his league leading eight goal of the season but was substituted seven minutes later with muscle problems in his right leg. It was confirmed Messi will be out for two to three weeks with a tear to his biceps femoris in his right leg.
On 1 October, Barcelona defeated Scottish club Celtic at Celtic Park with a 0–1 scoreline to stay at top of Group H in the Champions League. Fàbregas' goal gave Barça the win, a year after last season's defeat in the same fixture. On 5 October, Barcelona made it eight out of eight in their record breaking start to the league season with a 4–1 win over Real Valladolid at Camp Nou. Goals by Xavi, Neymar and a brace by Sánchez turned the result around after Valladolid's Javi Guerra opener in the tenth minute. On 19 October, Barcelona drop their first points of the season after a goalless draw with Osasuna at El Sadar that draw mean Barça failed to match La Liga's best ever start to a season and put an end to an eight-game winning run. On 22 October, Barcelona failed to clinch a spot in knockout rounds of the Champions League against Milan after a 1–1 draw in Italy. Messi goal equaled the result after Robinho opener in the ninth minute. With the draw, Barça stayed top of Group H with seven points, two more than Milan. On 26 October, the first Clásico of the season was contested at the Camp Nou with Barça securing a 2–1 victory over their great rivals. Strikes from Neymar and a spectacular Sánchez second gave Barça the win that leaves them six points clear of Real Madrid. On 29 October, Barcelona defeated Celta de Vigo 3–0 at Balaídos with goals from Sánchez and Fàbregas to keep Barça undefeated in the league.