The operation on Charlie resulted in rapid development of his intellect. It took a while before Charlie started to recognize the results of the operation. However, he made progress and got smarter. He learned new things and started to understand his environment and relationships better.

After the operation, Charlie was able to beat Algernon, the mouse who earlier underwent the same operation. He got better at reading and writing. Charlie also got to know that those he considered his friends were only out to make fun of him.

Then I walked home. It's a funny thing I never knew that Joe and Frank and the others liked to have me around all the time to make fun of me.

Charlie’s progress became noticeable, and his workmates became frightened of his new status. He was eventually dismissed from his workplace because of his new condition. He studied the experiment performed on him and realized that his progress was not permanent. His research improved on what the doctors knew. In a way, he made his mark on science, an achievement that made him proud.

Anyway I bet 1m the first dumb person in the world who ever found out somthing importent for sience. I remember I did somthing but I dont remember what. So I gess its like I did it for all the dumb pepullike me.

The largest overall affect that the operation has on Charlie is, of course, his rapidly growing intellect and IQ.  He quickly outpaces the doctor's expectations for the success of the procedure; the author effectively showcases Charlie's rapid rise in both observation and intellect through Charlie's own entries.  He becomes much more self-aware, and unfortunately with this his new found self-awareness, begins to realize that much of his situation which he once found comfortable, such as his old job and 'friends,' he can now no longer tolerate given his higher intellect.  Another side effect to the operation which Charlie also finds disturbing and troublesome is his developing sexual awareness, which makes the young man acutely uncomfortable in multiple social situations.