A product of the club's youth setup, Bannigan played his first professional season on loan at the then Scottish Second Division side Ayr United.

playing in the U17s side, Bannigan made his first team debut as a substitute on 24 July 2010 against Clyde in the Scottish Challenge Cup.

On 4 November 2010 Bannigan joined Scottish Second Division side Ayr United on a one-month loan deal.

[7] Bannigan made 24 Appearances scoring 4 goals to help Ayr gain promotion to the Scottish First Division via the play-offs.

[14] He was substituted during the extra-time period of the 2013 Scottish Challenge Cup Final, which Thistle lost to Queen of the South.

In early 2020, under the new management of Ian McCall, Bannigan penned a new 2-year contract extension, to remain at Partick Thistle until 2022, which would see him earn a testimonial at the club due to his decade of service.

[24] After winning Scottish League One with the Jags in 2020–21, Bannigan (now the longest-serving player) signed a new contract adding an extra year to his deal, extending it until 2023.

[25] In 2022, it was announced that alongside former teammate Chris Erskine, Bannigan would be inducted into the Partick Thistle Hall of Fame ahead of a testimonial to take place the following year.

[26] Bannigan scored his first goal of the 2023–24 season with a 25-yard volley into the top corner, in a 3–0 away win over Premiership side Ross County in the Scottish Cup.