The university ranking is normally published every year by the Center for World University Rankings (CWUR) and some of the yardstick used in ranking the universities in the world are accreditation, research, alumni employment, their offering of at least four years course, graduate and post-graduate course among a host of others. Below is the list of the first 300 universities ranking in Africa and not the world ranking.
UNIVERSITIES RANKING IN AFRICA

1. University of Cape Town              

2. University of the Witwatersrand

3. Stellenbosch University

4. University of Pretoria

5. Cairo University

6. University of Kwazulu Natal

7. University of Johannesburg

8.  University of South Africa

9.  University of the Western Cape

10. University of Nairobi

11. North West University

12. Alexandria University

13. Rhodes University

14. Makerere University

15. American University in Cairo

16. University of Ghana

17. University of Ibadan

18. Mansoura University

19. Addis Ababa University

20. University of the Free State

21. Ain Shams University

22. Université Cadi Ayyad Marrakech

23. Kenyatta University

24. Kwame Nkrumah University of Science & Technology

25. University of Nigeria

26. Covenant University Ota

27. Benha University

28. Assiut University

29. Zagazig University

30. Université Mohammed V de Rabat

31. University of Dar Es Salaam

32. University of Tanta

33. University of Zimbabwe

34. Helwan University

35. Tshwane University of Technology

36. Université des Frères Mentouri Constantine 1 (Ex Université Mentouri)

37. Al Azhar University

38. Obafemi Awolowo University

39. Moi University

40. Jimma University

41. University of Lagos

42. Kafrelsheikh University

43. Nelson Mandela University

44. Ahmadu Bello University

45. University of Zambia

46. Universidade Eduardo Mondlane

47. Mbarara University of Science and Technology

48. Minia University

49. University of Mauritius

50. Université Abou Bekr Belkaid Tlemcen

51. Cape Peninsula University of Technology

52. Université d'Oran 1 Ahmed Ben Bella

53. Arab Academy for Science & Technology and Maritime Transport

54. Minufiya University

55. University of Fort Hare

56. Université Mohammed Premier Oujda

57. University of Botswana

58. Beni Suef University

59. Djillali Liabes University of Sidi Bel Abbes

60. Fayoum University

61. British University in Egypt

62. Université Setif 1 Ferhat Abbas Setif

63. Jomo Kenyatta University of Agriculture and Technology

64. South Valley University

65. University of Ilorin

66. Université de Bejaia

67. University of Cape Coast

68. Université de Batna

69. German University in Cairo

70.Université Sidi Mohammed Ben Abdellah Fes

71. Université Mohamed Khider Biskra

72. Federal University of Technology Akure

73. University of Khartoum

74. University of Limpopo

75. Université d'Abomey Calavi

76. Muhimbili University of Health and Allied Sciences

77.University of Malawi College of Medicine Liverpool Wellcome Trust

78. Université Cheikh Anta Diop de Dakar

79. Université de M'Sila

80. Université Hassan II de Casablanca

81. Sokoine University of Agriculture

82. Adekunle Ajasin University

83. Mekelle University

84. Bahir Dar University

85. Université des Sciences et de la Technologie Houari Boumediene

86. Suez Canal University

87. Université Ibnou Zohr d'Agadir

88. University of Port Harcourt

89. Université Badji Mokhtar de Annaba

90. Université de Sfax

91. University of Rwanda

92. University of Venda

93. Zewail City of Science and Technology

94. Université des Sciences et de la Technologie d'Oran Mohamed Boudiaf

95. Federal University of Technology Minna

96. Nile University

97. Université de Tunis El Manar

98. University of Namibia

99. Aswan University

100. University for Development Studies

101. University of Benin

102. Durban University of Technology

103. Sohag University

104. Université Abdelhamid Ibn Badis Mostaganem

105. Université Moulay Ismail Meknès

106. Sudan University of Science & Technology

107. Université de Dschang

108. Université de Jijel

109. Université M'Hamed Bougara de Boumerdes

110. Al Akhawayn University Ifrane

111. Vaal University of Technology

112. Egerton University

113. Ladoke Akintola University of Technology

114. Université Abdelmalek Essaadi

115. Bayero University Kano

116. Université de Ouagadougou

117. University of Calabar

118. Université Chouaib Eddoukali

119. University of Malawi

120. Central University of Technology

121. Federal University of Technology Owerri

122. Nnamdi Azikiwe University

123. Université Hassiba Benbouali de Chlef

124. Rivers State University of Science & Technology

125. Université de Tébessa

126. University of Jos

127. University of Gondar (College of Medical Sciences)

128. Lagos State University

129. Damietta University

130. Namibia University of Science and Technology (Polytechnic of Namibia)

131. Université Ibn Tofail Kénitra

132. Port Said University

133. Université Amar Telidji de Laghouat

134 University of Uyo

135. Université 08 Mai 1945 Guelma

136. Université de Tunis

137. Haramaya University (Alemaya)

138. Walter Sisulu University

139. MISR University for Science & Technology

140. Ardhi University

141. Université de Carthage (7 de Novembre)

142. Olabisi Onabanjo University (Ogun State University)

143. Université de Monastir

144. Université Kasdi Merbah Ouargla

145. Université de Mascara

146. University of Benghazi (University of Garyounis)

147. University of Zululand

148. Pharos University in Alexandria

149. Hawassa University (Debub University)

150. Midlands State University

151. University of Agriculture Abeokuta

152. Damanhour University

153. Suez University

154. University of Buea

155. Université Internationale de Rabat

156. University of Abuja

157. Université Ibn Khaldoun Tiaret

158. Strathmore University Nairobi

159. Maseno University

160. Université de Sousse

161. Université Mouloud Mammeri de Tizi Ouzou

162. University of Maiduguri

163. Université Taher Moulay de Saida

164. Université d'Antananarivo

165. Université Larbi Ben Mhidi de Oum El Bouaghi

166. Université de Lomé

167. University of Tripoli (Al Fateh University)

168. University of Swaziland

169. Usmanu Danfodiyo University

170. Université Dr Yahia Farès de Médéa

171. Université d'Eloued

172. Gezira University

173. Université Saad Dahlab Blida

174. Université d'Alger 1

175. Kyambogo University

176. Université de la Manouba

177. University of Dodoma

178. Egypt Japan University of Science & Technology

179. Misurata University (Misrata University)

180. Higher Technological Institute

181. Bindura University of Science Education

182. Institut Agronomique et Veterinaire Hassan II

183. École Nationale Polytechnique d'Alger

184. Université de Gabes

185. Institut National des Postes et Telecommunications Maroc

186. Université Ziane Achour de Djelfa

187. National University of Science & Technology

188. Gulu University

189. Chinhoyi University of Technology

190. Abubakar Tafawa Balewa University

191. Masinde Muliro University of Science & Technology

192. National University of Lesotho

193. Université de Tunis Institut Supérieur de Gestion de Tunis

194. Afe Babalola University Ado Ekiti

195. Neelain University

196. Copperbelt University

197. Libyan International Medical University

198. University of Education Winneba

199. Université de Bouira

200. Université de Béchar

201. Université de Ngaoundéré

202. Murang’a University of Technology

203. Military Technical College

204. Université de Skikda

205. Sebha University /Sabha University

206. Université de Jendouba Ecole Supérieure d'Agriculture du Kef

207. Catholic University of Health and Allied Sciences (Weill Bugando University College)

208. Université Mohamed Chérif Messaadia de Souk-Ahras

209. Open University of Tanzania
bandera

210. Mzumbe University

211. Federal University of Petroleum Resources Effurun

212. Kampala International University

213. Université de Yaounde I

214. Université de Carthage Institut National des Sciences Appliquées et de la Technologie

215. American University of Nigeria

216. Université Hassan I Settat

217. Benue State University

218. Université Mohamed El Bachir El Ibrahim Bordj Bou Arréridj

219. Ashesi University

220. Niger Delta University

221. University of Technology Mauritius

222. Tumaini University Makumira

223. University of Mines & Technology Tarkwa

224. African University of Science & Technology Abuja

225. Federal University of Agriculture Makurdi

226. MISR International University

227. Université Sultan Moulay Slimane Beni Mellal

228. Federal University Oye Ekiti Ekiti State

229. Université de Khenchela

230. Université de Carthage Ecole Supérieure des Industries Alimentaires de Tunis

231. Université Félix Houphouët Boigny (Université de Cocody Abidjan)

232. United States International University

233. Omdurman Ahlia University

234. Université du Burundi

235. Catholic University of Eastern Africa

236. Daystar University

237. Delta State University Nigeria

238. Arsi University

239. Monash University South Africa

240. Mzuzu University

241. Landmark University

242. École National Supérieure de l'Informatique (ex-INI)

243. Technical University of Kenya

244. MTI University (Modern University for Technology and Information)

245. Université Gaston Berger de Saint Louis

246. Omar Al Mukhtar University

247. International University of Africa

248. Babcock University

249. Great Zimbabwe University

250. Université de Lubumbashi

251. Michael Okpara University of Agriculture Umudike

252. Uganda Martyrs University

253. Université de Gafsa

254. Busitema University

255. Garden City University College

256. Mkwawa University College of Education

257. Federal University Ndufu Alike Ikwo FUNAI

258. Nelson Mandela African Institute of Science & Technology

259. Islamic University in Uganda

260. Harare Institute Technology

261. Delta University for Science & Technology

262. Universidade Pedagógica

263. Mount Kenya University

264. Cross River State University of Science & Technology Calabar

265. Zimbabwe Open University

266. Universidade Católica de Moçambique

267. Redeemer's University

268. Osun State University

269. 2iE International Institute for Water and Environmental Engineering

270. Uganda Christian University

271. Ghana Institute of Management and Public Administration

272. Mahatma Gandhi Institute Rabindranath Tagore Institute

273. Skyline University Nigeria

274. Universidade Agostinho Neto

275. Université de Tunis el Manar Ecole Nationale d'Ingénieurs de Tunis

276. Université de Jendouba

277. State University of Zanzibar

278. Federal Polytechnic Ilaro

279. Africa University

280. Future University

281.Université Abdou Moumouni de Niamey

282. Michael Okpara University of Agriculture Umudike

283. Kwara State University

284. Imo State University Owerri

285. University of Sierra Leone

286. Joseph Ayo Babalola University

287. South Eastern Kenya University

288. Omdurman Islamic University

289. Abia State University Uturu

290. Kibabii University

291. Bowen University

292. Ghana Telecom University College

293. Makerere University Business School

294. Federal University Dutsin Ma

295. Université de Constantine 2

296. Umaru Musa Yar'Adua University (Katsina State University)

297. Nigerian Defence Academy Kaduna

298. Institution de la Recherche et de l'Enseignement Supérieur Agricoles

299. Alzaiem Alazhari University

300. Pwani University

Friends sorry for the long list, it is just to make sure that a substantial amount of Nigerian universities were captured in the list. The universities that didn't show up in this list are those below the rank of 300 and below.