Wee, who speaks Malay, English and Mandarin, begin his political career in the Johor Bahru Malaysian Chinese Association, which he joined in 1992.. He was its Secretary General from 1993 to 2005. After that, he is elected as Johor Bahru's MCA Majidi Branch chairman from 1996 to 2008, and became the MCA Johor Bahru Division Youth Chief from 2002 to 2008. In 2005 during the National MCA Youth election, he was elected as the National MCA Youth Wing Secretary General, and was appointed as the National MCA Youth Education Bureau Chief. He was awarded The Outstanding Young Malaysian Award by the Junior Chamber International Malaysia; this award was presented to him by Dato' Sri Ong Tee Keat, then Deputy Minister of Youth and Sports, in Kuala Lumpur on 25 November 2005. On 13 October 2008, Wee was elected unopposed as the MCA Youth Chief for the 2008–2011 term, taking over the position from the Health Minister, Dato' Sri Liow Tiong Lai. On 11 November 2008, Wee Ka Siong was elected to lead the MCA Malacca State Liaison Committee. Prior to this, he was the secretary general for Malaysia Chinese Association Youth Wing. In 2013, he contested, and won, the deputy presidency of the full party.
Deputy Education Minister (2008–2013)
Under the Prime Minister, Datuk Seri Najib Tun Razak, he was given the mandate to continue leading the Education Ministry as a Deputy Education Minister along with Dr. Mohd Puad Zarkashi. Its Education minister is the former Deputy Prime Minister of Malaysia, Tan Sri Muhyiddin Yassin. As minister, he reversed the decision to close the SJKC Damansara School, closed in 2001 because it "no longer provided a conducive learning environment because of traffic jams and noise pollution" due to a nearby trunk road. Its closure was opposed by some parents, who refused to transfer their children to its replacement. When it reopened in late 2009, it was renamed 'SJKC Chung Hwa'. He was given the mandate by the cabinet to handle and execute the Government's stimulus package in November last year that RM200mil will be given out in equal measure to Chinese, Tamil, religious and Mubaligh schools.
Cabinet Minister (2014–2018)
After the MCA's disastrous performance in the 2013 election, losing eight of its fifteen seats, the MCA voluntarily withdrew from its ministerial positions. The party returned in 2014 and Wee, by then the deputy president of the party, was appointed to the Cabinet as Minister in the Department of Prime Minister Najib Razak. After months of public speculations about Wee's health, on 2 May 2016 he made a statement that he would undergo a spinal surgery abroad and promised he will recover and return to duty soon. Wee Ka Siong is the only member of MCA to hold a seat in the parliament after the Malaysian general election in May 2018. On 22 August, Wee Ka Siong publicly announced that it is better for Malaysia to proceed with the ECRL and Gas Pipeline projects instead of postponing it because he believes it will adversely affect ties with China.