Sadie Henry, 28, continued to see Cameron Rose after three-year-old Rhys died from head injuries.
She had found the little boy blue in the face after leaving him alone with Rose at her flat in Erith, Kent, in January last year.
She told the Old Bailey she continued seeing Rose for sex until she was arrested and cautioned for trying to cover up the relationship.
Rose, now 18, of Eltham, south-east London, denies murder and assault charges.
Miss Henry told jurors: "I felt guilty because my three-year-old son died and the person I cared about saw him die.
"I thought he died from natural causes. I thought I should have been there."
Miss Henry, who also has an older child, denied she was obsessed with Rose but agreed she had hacked into his Facebook account when he tried to call off the relationship a month before Rhys's death.
Under cross-examination, she denied she cared more about the affair than looking after her children.
But she agreed she had pursued Rose after they met briefly at a party and had sex with him shortly after inviting the schoolboy to her home in November 2010.
She said: "I was attracted to him. I didn't see the consequences. I was not obsessed. I cared about him. At the time I thought the feeling was mutual.
"I didn't know I was hurting my children in the process. I was having fun for the first time."
The case is ongoing.
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