In 2015, if you have been frequently visiting our  university ranking page you would have noticed  that kenyayote  has released more than six rankings of top Kenya universities. The rankings are done by different organizations and the mode of rankings differ from one organization to another.
Some organization rely on web metrics to ranks universities, others depend on the infrastructure to rank universities. That is why you will find one organization ranking moi university the second best university in Kenya and the other ranking Kenyatta University the second best university in Kenya.
Now that you have an understanding why the rankings differ lets look at the 2015 Ranking for African Universities and Higher Institutions according to Journals consortium rankings.

The Journals consortium organization university rankings are based based on research publications and citations  of a university from the last five years (2010 to 2014) and its visibility on the internet.

1. University of Nairobi     (42.81)
2. Kenyatta University     (32.05)
3. Moi University     Eldoret  (26.03)
4. Jomo Kenyatta University of Agriculture and Technology (22.74)
5. Egerton University     (22.35)
6. Maseno University     (16.36)
7. Catholic University of Eastern Africa     (10.22)
8. Masinde Muliro University of Science and Technology         (10.05)
9. Strathmore University     (9.53)
10. United States International University (9.41)
11. Kabarak University     (9.36)
12. Mount Kenya University  (8.68)
13. Kenya Methodist University         (8.09)
14. Daystar University         (7.33)
15. University of Eldoret         (7.12)
16. Kisii University     (7.11)
17. KCA University     (6.42)
18. Pwani University     (6.38)
19. Kenya Institute of Management     (6.30)
20. Chuka University     (6.27)
21. African Virtual University         (5.91)
22. Technical University of Kenya     (5.59)
23. South Eastern Kenya University         (5.28)
24. University of Eastern Africa         (5.26)
25. Kenya Medical Training College         (5.18)
26. Great Lakes University     Kisumu     (5.05)
27. Jaramogi Oginga Odinga University of Science and Technology         (4.87)
28. Karatina University     (4.78)
29. Africa International University     (4.76)
30. Dedan Kimathi University of Technology         (4.45)
31. Africa Nazarene University         (4.33)
32. Technical University of Mombasa         (4.08)
33. Tangaza College         (3.96)
34. Maasai Mara University     (3.57)
35. University of Kabianga     Kericho     (3.36)
36. Management University of Africa         (3.01)
37. Multimedia University of Kenya     (2.68)
38. Taita Taveta University College         (2.57)
39. Institute of Advanced Technology     (2.52)
40. Rongo University College     (2.46)
41. Laikipia University College         (2.40)
42. Presbyterian University of East Africa         (2.33)
43. The Presbyterian University of East Africa          (2.33)
44. Meru University of Science and Technology         (2.22)
45. Inoorero University         (2.21)
46. Adventist University of Africa         (2.19)
47. Zetech College     Nairobi     (2.08)
48. Nairobi Institute of Business Studies         (2.00)
49. Riara University     Nairobi     (1.99)
50. Kenya Highlands Evangelical University         (1.95)

The above rankings are based on Journals Consortium a united states based online a company dedicated to providing resources to the academic community. The points you are seeing infront of each university indicates its Total influencer factor.

For more information about Journals Consortium  2015  Top 50 Universities in Kenya rankings check out here.