What will be the brokerage?

In a single day,

1st trade - I am buying 1000 shares of X @ 250 and sells @ 251, here i understand that the brokerage is 40 rs (including buy and sell).

2nd trade in a same day - buy 200 shares of X @ 249 and sells @ 250, what will be the brokerage either 10.02 or 40 rs. In a simple way is that 0.01% brokerage is applicable to that particular order turnover or a days total turnover.

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To simply put, (considering you trade with Zerodha) the brokerage is per order vise, not turnover based one.

In your example case, your brokerage would be roughly 20+20+5+5 =50 INR.

This is what Zerodha calculator indicates and my contract notes too.

Brokerage per order from 0.01 % to 20 Rs , which ever is less.

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Brokerage would be 40 since these trades would result in 4 orders, 2 order per trade. Brokerage is applied per order and not per trade.

Checkout http://zerodha.com/brokerage-calculator

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Simple, every executed order is Rs. 20/- (BUY - 20/- plus SELL 20/-), so total Rs. 40/- for your first BUY/SELL. Similarly, your second BUY/SELL is also Rs. 40/-

So, total brokerage is Rs. 80/- for the full day.

(P.S. I have not considered STT, Service Tax, Cess…etc)

1st trade - I am buying 1000 shares of X @ 250 and sells @ 251, here i understand that the brokerage is 40 rs (including buy and sell).

Agreed. Brokerage is 40. Your understanding is correct.

2nd trade in a same day - buy 200 shares of X @ 249 and sells @ 250, what will be the brokerage either 10.02 or 40 rs. In a simple way is that 0.01% brokerage is applicable to that particular order turnover or a days total turnover.

Yes. You are right. 0.01% brokerage is applicable for every separate order's turnover. Not for the entire day's turnover. So you will be charged (249+250) x 200 x 0.01% = 9.98 for this second trade. Note: For Intraday, your single order includes both Buy and Sell, so you need to add 249x200 and 250x200 together and see that as your turnover for brokerage purpose.