This only referendum in Singapore's history was to decide the terms and conditions on the merger with Malaysia. Singapore's political parties were permitted to campaign for the different options starting from 14 August 1962. PAP stood for "A", where Singapore would retain autonomy over education, labour and language policies, while all citizens would automatically become Malaysian citizens but Singapore would have a fixed number of seats in the Federal Parliament. Option "B" stipulated that the status of Singapore would be equal to former Straits Settlements of Penang, Malacca and other Malayan states. Seats in the Federal Parliament would be allocated on proportional representation basis. SPA, which was friendly with Malaysia's ruling Alliance Party, stood for "C", where Singapore would enter under no less terms than the North Borneo territories of Sabah and Sarawak, which were also joining the merger. For "B" and "C", only those born in Singapore and their descendants could directly become citizens of Malaysia. As there was no option to reject merger, coupled with the uncertain citizenship status of Singaporeans, the referendum was criticised as a "sham" by Barisan, LSP, WP, UDP, PR and UPP. Barisan further opposed the inclusion of the North Borneo states. These parties called on voters to cast blank votes and with the exception of SPA and UPP, formed a Council of Joint Action to appeal to the United Nations. After the citizenship matter was resolved, LSP pulled out of CJA as it felt its purpose was achieved and preferred the referendum be scrapped, while WP's position became untenable due to internal party friction. In the end, "A" received a resounding endorsement, symbolising victory for PAP. At the following Legislative Assembly sitting after the referendum, Prime Minister Lee Kuan Yew responded to accusations of Barisan about the undemocratic process by tabling a bill to include the blank and unclear votes in any one of the three options chosen by the legislature. PAP and SPA lawmakers abstained from voting but neither did those from Barisan, who instead staged a walk-out during the sitting.

Polling day: 1 September 1962 [Sat]

Electorate: 619,867
Voter turnout: 561,559 (90.6%)

"I support merger giving Singapore autonomy in labour, education and other agreed matters as set out in Command Paper No. 33 of 1961, with Singapore citizens automatically becoming citizens of Malaysia."
People's Action Party
397,626 (95.8%)
"I support complete and unconditional merger for Singapore as a state on an equal basis with the other eleven states in accordance with the Constitutional documents of the Federation of Malaya."
9,422 (2.3%)
"I support Singapore entering Malaysia on terms no less favourable than those given to the Borneo territories."
Singapore People's Alliance
7,911 (1.9%)
Votes for merger
[A + B + C]
414,959 (73.9%)  
Blank votes 144,077 (25.7%) Barisan SosialisUnited People's PartyPartai RakyatUnited Democratic Party
Unclear votes 2,523 (0.4%)