Let G be a finite group, let H be a core-free subgroup and let b(G, H) denote the base size for the action of G on G/H. Let $$\alpha (G)$$
α
(
G
)
be the number of conjugacy classes of core-free subgroups H of G with $$b(G,H) \ge 3$$
b
(
G
,
H
)
≥
3
. We say that G is a strongly base-two group if $$\alpha (G) \le 1$$
α
(
G
)
≤
1
, which means that almost every faithful transitive permutation representation of G has base size 2. In this paper, we study the strongly base-two finite groups with trivial Frattini subgroup.