| Date | Title of the agreement |
| 1922.11.30 | Tonnage Measurement of Merchant ships |
| 1923.07.27 | Tonnage Measurement of Merchant ships |
| 1953.03.27 | Tonnage Measurement of Merchant Ships (revival of agreement 1922.11.30) |
| 1955.09.21 | Agreement regarding British Commonwealth War Graves in Japanese territory |
| 1962.06.20 | Agreement to place source materials transferred from South Africa t Japan under the safeguard of the IAEA (Nuclear Energy) |
| 1963.04.06 | Parcel Post Agreement |
| 1977.09.30 | Exchange of Notes concerning the Return to Japan of Certain Portions of the Land Granted to the Commonwealth War Graves Commissions for use as the British Commonwealth War Cemetery at Yokohama, under and Agreement signed on 1955.09.21 |
| 1977.12.06 | Agreement on Fisheries |
| 1992.01.13 | Notes Verbal and Exchange of Notes concerning the Re-establishment of Diplomatic Relations |
| 1994.03.08 | Air Services Agreement |
| 1995.11.30 | Agreement to Confer Immunities and Privileges upon Transferred Officials of the Japan International Fund (JICA) and the Overseas Economic Co-operation Fund (OECF) |
| 1996.04.30 | Agreement of Notes Constituting an Agreement regarding a Yen 9,000,000 and a Yen 3,097,000,000 loan to be extended with a view of Prompting the Economic Stabilisation and Development efforts of the Government of the Republic of South Africa |
| 1997.03.07 | Convention for the Avoidance of Double Taxation and the Prevention of Fiscal Evasion with respect to Taxes on Income, plus Protocol, plus Exchange of Notes |
| 1997.06.12 | Exchanging of Notes on Japanese Grant Assistance for Improvement of Medical Equipment for Hospitals in the Republic of South Africa |
| 1998.02.19 | Exchange of Notes concerning a Japanese Loan for the Urban Rail Passenger Transport Modernisation Project |
| 1998.04.09 | Exchange of Notes concerning Japanese Loan for the Rural Social Infrastructure Programme (I) |
| 1999.01.15 | Exchange of Notes in respect of construction of Primary and Junior Secondary Schools in the Eastern Cape |
| 1999.08.31 | Exchange of Notes concerning Japanese Economic Co-operation for the Execution of the Project for the Construction of Primary and Junior Secondary Schools in the Eastern Cape Province |
| 2000.08.23 | Exchange of Notes in respect of the Promotion of Cultural Activities in the RSA (Lighting Equipment for the Market Theatre) |
| 2001.01.09 | Exchange of Notes in respect of the Japan Overseas Co-operation Volunteers in the Republic of South Africa |
| 2001.02.07 | Exchange of Notes concerning the Master Plan Study on Tourism Development |
| 2001.03.10 | Exchange of Notes concerning the Study of the Development of Small and Medium Enterprise in Kwa-Zulu |
| 2001.09.10 | Exchange of Notes concerning the second Project for Construction of Primary and Junior Secondary Schools in the Eastern Cape |
| 2002.01.16 | Exchange of Notes on the Project for the Improvement of health Facilities in Kwazulu-Natal |
| 2003.08.28 | Science and Technology Agreement |
