During that time, he served near-continuously in the Executive Council of Limpopo, holding several different portfolios under Premiers Ngoako Ramatlhodi and Sello Moloto.

After joining the National Assembly in the 2009 general election, Motsoaledi was appointed as Minister of Health in the cabinet of President Jacob Zuma.

He held the position throughout Zuma's presidency, during which time he developed the policy and legislative framework for a new system of National Health Insurance.

He also presided over a transformation in South Africa's policy on HIV/AIDS and a concomitant four-fold expansion in the size of the country's antiretroviral programme.

Zuma's successor, President Cyril Ramaphosa, appointed Motsoaledi as Minister of Home Affairs after the 2019 general election.

[2] After matriculating at the Setotolwane High School, Motsoaledi completed a pre-medical course at the University of the North at Turfloop, where he was involved in anti-apartheid student politics.

[2] He went on to study medicine at the University of Natal, where he served on the medical school's student representative council from 1980, succeeding Zweli Mkhize as its president in 1982.

[2] He was also a founding member of the Azanian Students' Organisation (AZASO) and was elected as its national correspondence secretary, serving under president Joe Phaahla.

[2] When the ANC was unbanned in 1990 during the negotiations to end apartheid, Motsoaledi became involved in running the party's overt structures in the Northern Transvaal.

[5] However, he returned to the Executive Council on 24 August 1998, when Ramatlhodi appointed him to succeed Benny Boshielo as MEC for Transport;[8] his reappointment reportedly followed an intervention by ANC deputy president Jacob Zuma.

[14] In the 2009 general election, Motsoaledi did not seek re-election to the Limpopo Provincial Legislature but instead won a seat in the National Assembly, the lower house of the South African Parliament.

[21] He also appointed a ministerial task team to investigate maladministration at the Health Professions Council of South Africa, leading in 2016 to several high-level dismissals.

[24] In domestic politics, however, towards the end of his tenure, critics accused him of hostility towards non-citizen residents,[25][26][27] with a Sunday Times editorial remarking in March 2019 that he had "earned something of a reputation in the foreigner-bashing department".

[28] Many observers, even those who were critical of the broader functioning of the healthcare system during Motsoaledi's tenure, praised him for his impact on HIV/AIDS policy, which they labelled his greatest achievement and legacy.

[29][30] Continuing the work of his predecessor, Motsoaledi set about "undoing the damage"[31] wrought by Thabo Mbeki's health minister, Manto Tshabalala-Msimang, who was frequently accused of HIV/AIDS denialism.

[30] By August 2011, the Treatment Action Campaign said of Motsoaledi, "We've seen a massive change since the Manto years – he listens and he understands the challenges we face in HIV/Aids.

[29] His department announced a switch to a fixed-dose combination ARV, efavirenz/emtricitabine/tenofovir, in 2012,[40] and Motsoaledi launched the new treatment regimen in April 2013 in Ga-Rankuwa.

[29] Apart from HIV/AIDS, the central policy initiative of Motsoaledi's term was the new National Health Insurance (NHI) proposal, which would aim to provide universal healthcare to all legal residents.

[45] Upon taking office in 2009, he appointed a 25-member advisory committee on the initiative,[46] culminating in a green paper on NHI which was approved by the cabinet in August 2011 and which suggested a 14-year implementation timeframe.

[52] In early 2012, he warned that his department would "be making a lot of noise" about smoking, alcohol consumption, diet, and exercise, which he said were key factors in South Africa's high burden of non-communicable diseases.

[78] However, at the end of 2022, the Mail & Guardian criticised him for inaction on his plan to effect a "complete overhaul of the immigration system", which he had announced at the beginning of the year.