In 2002–03 he made his league debut in Serie B. This marked the beginning of the two competitive seasons he played as a starter in Salerno, that included his first professional goal in 2004–05 in a match against Bari. In 2005, he moved to Siena, a club that he played for two seasons.
In 2005, he was noticed by the dense network of observers of Juventus and signed, who decided to sell him in co-ownership to Siena, in which Juventus already had several players on loan. He made his debut in Serie A on 18 September 2005 in Siena - Palermo 1–2 and his first season in the top FLIGHT was characterised by ups and downs; losing the role of starting left-back to the more experienced Gianluca Falsini.
For 2006–07, Juventus, relegated to Serie B by the 2006 Italian football scandal, allowed Molinaro to remain at Siena (who sold Falsini), relying on him to cover the role of left-back. He collected 36 appearances out of 38 league games and two appearances in 2 rounds of Coppa Italia.
On 20 June 2007, shortly before the transfer window deadline, Juventus redeemed him for a sum of €2.5 million. During 2007–08, at age 24, he carved out a starting spot on the left wing of the defence of Juventus, thanks to the movement of companion Giorgio Chiellini to central defence.
In his second season at Juventus he debuted 13 August 2008 in the first leg of the third qualifying round of the Champions League, won 4–0 against Petržalka, which also represented his debut in European competition. On 28 November 2008 he extended his contract with Juventus until 2013. He finished the 2008–09 season prematurely because of a perirenal hematoma.
Molinaro received his first international call-up on 6 August 2010 under new head coach Cesare Prandelli. He made his debut on 10 August 2010, starting in the match against Côte d'Ivoire. He was also called up for the games against Estonia and Faroe Islands in the Euro 2012 qualifiers.
On 16 June 2014, Molinaro was signed by Torino on an annual contract. He made his debut with the Granata in the third round of the 2014–15 Europa League against Brommapojkarna. On 25 June 2015, Torino exercised the option to extend his contract.
