This article lists important figures and events in Malaysian public affairs during the year 1999, together with births and deaths of notable Malaysians.

• 1 January – Visit Negeri Sembilan Year 1999 officially began
• January – Malaysia exited from economic crisis
• 15 January – Tan Sri Abdul Rahim Noor resigned as the Inspector General of Police after taking full responsibility for injuries suffered by former Deputy Prime Minister, Anwar Ibrahim while in police custody.
• February – Abdullah Ahmad Badawi became Deputy Prime Minister, replacing Dato' Seri Anwar Ibrahim.
• 3 March – Many federal administration sections were moved to the new federal administrative centre in Putrajaya, but Kuala Lumpur remained the capital.
• 4 March – Sultan Mizan Zainal Abidin was crowned as Sultan of Terengganu.
• 10 March – Baby dugong, Si Tenang was found dead by a fisherman in Pasir Gudang, Johor.
• 15 March – The Smart TAG on-board unit (OBU) was launched, replacing PLUS TAG
• 4 April – Parti Keadilan Nasional (Keadilan) was launched.
• 14 April – Dato' Seri Anwar Ibrahim was found guilty of corruption and sentenced to six years in jail.
• 16-18 April – 1999 Malaysian motorcycle Grand Prix
• 19 April – Two brothers, Justin Read, 19 and Gerald Read, 25 were the first Malaysians to reach the North Pole after encountering challenging weather.
• 20 April – The Sepang International Circuit, Malaysia's home of motorsports was officially opened.
• 26 April – Sultan Salahuddin Abdul Aziz Shah of Selangor was elected as the 11th Yang di-Pertuan Agong.
• May – Menara Alor Star, Alor Star first landmarks officially opened.
• 15 May – A landslide near Bukit Antarabangsa, Ulu Klang, Selangor. Most of the Bukit Antarabangsa civilians were trapped.
• 21 May – Sun Cruises' liner SS Galileo Galilei or also known as SS Sun Vista sank in the Straits of Malacca near Penang after the vessel suffered an engine room fire, which cut all power. All 1,090 passengers and crew were safely evacuated.
• 1 June – Section 2 of the PUTRA-LRT from Masjid Jamek to Gombak opened, containing Malaysia's first underground rail line.
• 21 June – Prime Minister, Mahathir Mohamad moved into new office at the Perdana Putra building in the new federal administrative centre in Putrajaya.
• 8 July – The official opening ceremony for the Multimedia Super Corridor (MSC) centre in Cyberjaya.
• 10 August – Azhar Mansor becomes the first Malaysian solo sailor to sail around the world by Jalur Gemilang sailing ship.
• 23 August – The establishment of University of Selangor in Selangor.
• 26 August – The Institut Teknologi MARA (ITM) was given its university status and renamed Universiti Teknologi MARA (UiTM).
• 31 August – The Petronas Twin Towers was officially opening ceremony by Prime Minister of Malaysia Tun Dr. Mahathir bin Mohamad in conjunction with Petronas celebrated its twenty-fifth year of anniversary with silver jubilee the,e and Independence Day celebrated its forty-second year of anniversary.
• September – Opening of the Istana Budaya in Kuala Lumpur.
• September – The Bintang Walk at Bukit Bintang was officially opened.
• 11 September – Sultan Salahuddin Abdul Aziz Shah of Selangor was installed as Yang di-Pertuan Agong.
• 1 October – Bank of Commerce merged with Bank Bumiputra Malaysia Berhad and changed its name to Bumiputra-Commerce Bank Berhad.
• 10 October – Opening of the Port of Tanjung Pelepas in Johor.
• 17 October – The first Formula One Petronas Malaysian Grand Prix held at the Sepang International Circuit.
• 25 October – Barisan Nasional celebrated its 25th anniversary.
• 18 November – Mid Valley Megamall, the largest shopping complex in Malaysia was officially opened.
• 18–21 November - World Cup Golf Malaysia 1999^[1]
• 29 November – The 1999 General Elections. Terengganu fall to the PAS party.^[2]
• 22 December – A Mutiara express bus caught fire after plunging into a ravine at Kampung Bayu in Paloh, near Gua Musang, Kelantan killing three passengers and injuring eight.

• 18 March - Muhammad Saiful Aiman Shaharudin – Badminton player
• 12 July – Nur Dhabitah Sabri – Diver
• 11 September – Nurin Jazlin – Murder victim (died 2007)
• 24 November - Muhammad Erry Hidayat – Weightlifter

• 2 February – Tunku Kurshiah binti Almarhum Tunku Besar Burhanuddin — Tunku Ampuan Besar Negeri Sembilan and first Raja Permaisuri Agong (born 1911)
• 15 July – Lee An Tong – Deputy Secretary General of the Malayan Communist Party (born 1917)

• 1999
• 1998 in Malaysia | 2000 in Malaysia
• History of Malaysia