McDonald joined Stoke City's academy from Manchester City's academy in 2005. He became a regular in the club's youth and reserves side but was released in the summer of 2010. In October 2009 he joined Nantwich Town on loan to gain some first team experience. However Stoke recalled McDonald after just one substitute appearance after academy manager Adrian Pennock wanted him to start on his debut.
McDonald signed for Oldham Athletic in early August 2010 after impressing in a series of trial games at the club. He made his debut on 31 August 2010 in a Football League Trophy match against Shrewsbury Town as a 45th-minute substitute. On 29 October 2010 he joined Stafford Rangers for a month-long loan period to gain some first team experience. He returned to Oldham at the end of November having made four appearances whilst on loan, including three league matches. On 22 February 2011, McDonald joined Northern Premier club Nantwich Town on a month-long loan deal. The loan was extended on 24 March until the end of the season. At the end of the season he was informed that he was out of contract and would not be offered a new deal.
On 28 January 2013, McDonald joined Hereford United on a contract lasting until the end of the season. After impressing Hereford manager Martin Foyle, McDonald signed a new one-year contract on 11 June 2013.
After leaving Telford United, Rod McDonald joined Northampton Town on a trial, and impressed manager Chris Wilder enough to earn a 12-month contract with the Cobblers. McDonald made his debut for Northampton in a 3–0 win over Exeter City on 15 August 2015, as a substitute for Zander Diamond. He eventually established himself as a regular starter in the side as they went on to win the 2015/16 League Two title, signing a new contract with the club until the summer of 2018 in February 2016. Following Chris Wilder's departure as Northampton Town manager in May 2016, Rod McDonald struggled to establish in the side during the following season in League One, making just nine appearances in all competitions during the 2016/17 season. At the end of the campaign, McDonald was transfer-listed by manager Justin Edinburgh, alongside three other players.
On 19 May 2017, Rod McDonald was signed by Coventry City on a two-year contract for an undisclosed fee. McDonald made his debut for the Sky Blues in a 3–0 victory over Notts County on the opening day of the 2017–18 League Two season.
AFC Wimbledon
On 2 August 2018, McDonald joined League One side AFC Wimbledon for an undisclosed fee.
Personal life
His father Rodney was a professional footballer, as is his older brother Clayton.
